tsoppy input standardization - 4. DNA and RNA alignment data

[danielvo]

Inputs considered so far:

• Dragen TSO500 analysis pipeline v. 2.6.2
  • the information below is based on output generated for samples sequenced with TSO500 assay version 2, but the current
  • unclear: is the Dragen server version a factor?
    • OUS assumes it does not, and both OUS and UNN use the same Dragen server version.
      • It looks like both assay v1 and assay v2 samples can now be analyzed with the same Dragen software.
    • Dragen server version [07.021.624.]3.11.2 was used when generating the output referenced in the text below
    • UNN utilizes the same Dragen server version and Dragen TSO500 analysis pipeline version
    • unclear: When analyzing samples with ICA (Illumina Cconnected Analysis), can one pick exactly the same Dragen server version and TSO500 pipeline version?
  • unclear: can the analysis output structure vary based on the sample sheet content/format choices?
    • different Pair_ID and Sample_ID values were used when generating the output referenced in the text below
    • we should aim to standardize the sample sheets across InPreD nodes either way
• Local App version 2.2.0.12
  • the sample sheet content/format (e.g., the Pair_ID value choice) can impact the analysis output structure
    • different Pair_ID and Sample_ID values were used when generating the output referenced in the text below

4. DNA and RNA alignment data

4.1. Input files

Dragen TSO500 2.6.2:

• A single alignment file per sample
  • file path for DNA alignments: Logs_Intermediates/DnaDragenCaller/<sample_ID>/<sample_ID>.bam

@HD	VN:1.4	SO:coordinate
@SQ	SN:chr1	LN:249250621
@SQ	SN:chr2	LN:243199373
@SQ	SN:chr3	LN:198022430
@SQ	SN:chr4	LN:191154276
@SQ	SN:chr5	LN:180915260
@SQ	SN:chr6	LN:171115067
@SQ	SN:chr7	LN:159138663
@SQ	SN:chr8	LN:146364022
@SQ	SN:chr9	LN:141213431
@SQ	SN:chr10	LN:135534747
@SQ	SN:chr11	LN:135006516
@SQ	SN:chr12	LN:133851895
@SQ	SN:chr13	LN:115169878
@SQ	SN:chr14	LN:107349540
@SQ	SN:chr15	LN:102531392
@SQ	SN:chr16	LN:90354753
@SQ	SN:chr17	LN:81195210
@SQ	SN:chr18	LN:78077248
@SQ	SN:chr19	LN:59128983
@SQ	SN:chr20	LN:63025520
@SQ	SN:chr21	LN:48129895
@SQ	SN:chr22	LN:51304566
@SQ	SN:chrX	LN:155270560
@SQ	SN:chrY	LN:59373566
@SQ	SN:chrM	LN:16569
@SQ	SN:GL000207.1	LN:4262
@SQ	SN:GL000226.1	LN:15008
@SQ	SN:GL000229.1	LN:19913
@SQ	SN:GL000231.1	LN:27386
@SQ	SN:GL000210.1	LN:27682
@SQ	SN:GL000239.1	LN:33824
@SQ	SN:GL000235.1	LN:34474
@SQ	SN:GL000201.1	LN:36148
@SQ	SN:GL000247.1	LN:36422
@SQ	SN:GL000245.1	LN:36651
@SQ	SN:GL000197.1	LN:37175
@SQ	SN:GL000203.1	LN:37498
@SQ	SN:GL000246.1	LN:38154
@SQ	SN:GL000249.1	LN:38502
@SQ	SN:GL000196.1	LN:38914
@SQ	SN:GL000248.1	LN:39786
@SQ	SN:GL000244.1	LN:39929
@SQ	SN:GL000238.1	LN:39939
@SQ	SN:GL000202.1	LN:40103
@SQ	SN:GL000234.1	LN:40531
@SQ	SN:GL000232.1	LN:40652
@SQ	SN:GL000206.1	LN:41001
@SQ	SN:GL000240.1	LN:41933
@SQ	SN:GL000236.1	LN:41934
@SQ	SN:GL000241.1	LN:42152
@SQ	SN:GL000243.1	LN:43341
@SQ	SN:GL000242.1	LN:43523
@SQ	SN:GL000230.1	LN:43691
@SQ	SN:GL000237.1	LN:45867
@SQ	SN:GL000233.1	LN:45941
@SQ	SN:GL000204.1	LN:81310
@SQ	SN:GL000198.1	LN:90085
@SQ	SN:GL000208.1	LN:92689
@SQ	SN:GL000191.1	LN:106433
@SQ	SN:GL000227.1	LN:128374
@SQ	SN:GL000228.1	LN:129120
@SQ	SN:GL000214.1	LN:137718
@SQ	SN:GL000221.1	LN:155397
@SQ	SN:GL000209.1	LN:159169
@SQ	SN:GL000218.1	LN:161147
@SQ	SN:GL000220.1	LN:161802
@SQ	SN:GL000213.1	LN:164239
@SQ	SN:GL000211.1	LN:166566
@SQ	SN:GL000199.1	LN:169874
@SQ	SN:GL000217.1	LN:172149
@SQ	SN:GL000216.1	LN:172294
@SQ	SN:GL000215.1	LN:172545
@SQ	SN:GL000205.1	LN:174588
@SQ	SN:GL000219.1	LN:179198
@SQ	SN:GL000224.1	LN:179693
@SQ	SN:GL000223.1	LN:180455
@SQ	SN:GL000195.1	LN:182896
@SQ	SN:GL000212.1	LN:186858
@SQ	SN:GL000222.1	LN:186861
@SQ	SN:GL000200.1	LN:187035
@SQ	SN:GL000193.1	LN:189789
@SQ	SN:GL000194.1	LN:191469
@SQ	SN:GL000225.1	LN:211173
@SQ	SN:GL000192.1	LN:547496
@SQ	SN:NC_007605	LN:171823
@SQ	SN:hs37d5	LN:35477943
@RG	ID:1	LB:TVD0016-D01-P01-A00	PU:1	SM:TVD0016-D01-P01-A00
@RG	ID:2	LB:TVD0016-D01-P01-A00	PU:2	SM:TVD0016-D01-P01-A00
@RG	ID:3	LB:TVD0016-D01-P01-A00	PU:3	SM:TVD0016-D01-P01-A00
@RG	ID:4	LB:TVD0016-D01-P01-A00	PU:4	SM:TVD0016-D01-P01-A00
@PG	ID: Hash Table Build	VN: 01.003.044.3.11.2-hv-8	CL: /opt/dragen/3.11.2/bin/dragen --build-hash-table true --output-directory /staging/illumina/DRAGEN_TSO500_2.6.2/ref_hashtable --ht-reference /staging/illumina/DRAGEN_TSO500_2.6.2/ref_hashtable/genome.fa --ht-num-threads 48 --ht-build-rna-hashtable true --enable-cnv true	DS: digest_type: 1 digest: 0x6C40717F ref_digest: 0xC2311E75 ref_index_digest: 0xB4307AF0 hash_digest: 0x8E6AAC7D
@PG	ID: DRAGEN HW build	VN: 18101306
@CO	TS:Fri Mar 20 13:09:31 2026
@CO	LC:e53a5d6a41fea6a2438e8a514
@CO	DRAGEN emulates the ReCo tool, without running it as a separate executable
@PG	ID:Reco	PN:Reco
@PG	ID: DRAGEN SW build	VN: 07.021.624.3.11.2	CL: /opt/edico/bin/dragen --ref-dir hashtable --output-directory DnaDragenCaller --output-file-prefix TVD0016-D01-P01-A00 --events-log-file events.csv --tso500-solid-umi true --umi-metrics-interval-file resource_bundle/small_variants/TSO_HRD_manifest_randomized.bed --tso500-solid-snv true --vc-sq-call-threshold=-1 --vc-target-bed resource_bundle/small_variants/TST500C_manifest.bed --vc-target-bed-padding 8 --vc-systematic-noise resource_bundle/small_variants/mean_gvcf_bq30_lowSQ_v1.0_systematic_noise_v2.bed.gz --vc-depth-annotation-threshold 100 --vc-homref-depth-filter-threshold 100 --tumor-fastq-list TVD0016-D01-P01-A00.fastq_list.csv --tumor-fastq-list-sample-id TVD0016-D01-P01-A00 --vc-somatic-hotspots resource_bundle/small_variants/pepe2_prior.vcf --vc-hotspot-log10-prior-boost 3.0 --vc-blacklist-bed resource_bundle/small_variants/pepe_blacklist_sorted.bed --qc-coverage-ignore-overlaps true --gc-metrics-enable true --qc-coverage-region-1 resource_bundle/small_variants/TST500C_CodingRegions_hg19.bed --qc-coverage-reports-1 callability --qc-coverage-tag-1 tmb --qc-coverage-region-2 resource_bundle/small_variants/TST500C_manifest.exon.bed --qc-coverage-tag-2 exon --qc-coverage-reports-2 cov_report --tso500-contam-vcf resource_bundle/contamination/Contamination.vcf --qc-contam-min-basequal 30 --qc-contam-min-mapq 30 --tso500-solid-cnv true --cnv-combined-counts resource_bundle/cnv/TSO500_DRAGEN_BASELINE_SOLID_matched_targets_v2.combined.counts.txt.gz --cnv-segmentation-bed resource_bundle/cnv/dragen_tso500_manifest_cnv_genes_predefined_cutoff_FFPE.bed --cnv-target-bed resource_bundle/cnv/TSO500_DRAGEN_TARGET_SOLID_matched_targets.bed --tso500-solid-msi true --msi-microsatellites-file resource_bundle/msi/references/microsatellites-TSO500-SOLID-concordant.list --msi-ref-normal-dir resource_bundle/msi/data/TSO500-Solid --tso500-use-combined-license true --tso500-cnv-enable-low-validation-filter false --logging-to-output-dir true --force	DS: Aligner.align-direction: 4 Aligner.aln-en-mask: 15 Aligner.aln-enable: 1 Aligner.backtrace-delay: 8 Aligner.bed-score-bonus: 0 Aligner.chicken: 0 Aligner.dedup-min-qual: 15 Aligner.disable-lfsr: 0 Aligner.en-alt-hap-aln: 1 Aligner.en-chimeric-aln: 1 Aligner.exon-jump-en: 1 Aligner.filt-clip1-pair: 10 Aligner.filt-clip1-unpr: -5 Aligner.filt-clip2-pair: 5 Aligner.filt-clip2-unpr: -10 Aligner.filt-min-qual: 0 Aligner.fix-overlap-mapq: 0 Aligner.gap-ext-pen: 1 Aligner.gap-open-pen: 6 Aligner.global: 0 Aligner.hard-clip-tags: 1 Aligner.hard-clips: 6 Aligner.hw-mapq-max: 250 Aligner.leftalign-mode: 2 Aligner.mapq-coeff: 152 Aligner.mapq-floor-1snp: 0 Aligner.mapq-max: 60 Aligner.mapq-min-len: 50 Aligner.mapq-strict-sjs: 0 Aligner.match-score: 1 Aligner.max-rescues: 1023 Aligner.max-stitch-olap: 48 Aligner.min-overhang: 6 Aligner.min-overhang-ann: 4 Aligner.min-score-coeff: 0.0 Aligner.mismatch-pen: 4 Aligner.no-align-score: -8388608 Aligner.no-ambig-strand: 1 Aligner.no-noncan-motifs: 1 Aligner.no-unclip-score: 1 Aligner.no-unpaired: 0 Aligner.paired-mate-info: 1 Aligner.pe-max-penalty: 255 Aligner.pe-orientation: 0 Aligner.pe-sample-max-insert: 65535 Aligner.resc-ifpair-len: 48 Aligner.resc-nopair-len: 0 Aligner.rescue-ceil-factor: 3 Aligner.rescue-hifreq: 0 Aligner.rescue-kmer-len: 32 Aligner.rescue-max-snps: 7 Aligner.rna-max-insert: 4000000 Aligner.rna-pair-pen-rat: 5.71875 Aligner.sample-mapq0: 1 Aligner.sec-aligns: 0 Aligner.sec-aligns-hard: 0 Aligner.sec-phred-delta: 0 Aligner.sec-score-delta: 0 Aligner.supp-aligns: 3 Aligner.supp-as-sec: 0 Aligner.sw-all: 0 Aligner.sw-burst-diffs: 1 Aligner.sw-early-max: 256 Aligner.sw-extra-intvl: 1 Aligner.unclip-score: 5 Aligner.unpaired-pen: 80 Aligner.xs-pair-penalty: 25 Mapper.ann-sj-max-indel: 10 Mapper.chain-diam-lim: 8 Mapper.chain-rad-lim: 5 Mapper.dark-base: 2 Mapper.edit-chain-limit: 29 Mapper.edit-mode: 0 Mapper.edit-read-len: 100 Mapper.edit-seed-num: 6 Mapper.filt-good-qual: 0 Mapper.filter-len-ratio: 4 Mapper.intvl-max-hits: 16 Mapper.intvl-min-chains: 8 Mapper.intvl-sample-hits: 16 Mapper.intvl-seed-length: 60 Mapper.intvl-seed-longer: 8 Mapper.intvl-target-hits: 32 Mapper.map-orientations: 0 Mapper.max-dram-reqs: 0 Mapper.max-hifreq-hits: 16 Mapper.max-intron-bases: 200000 Mapper.max-lowq-bases: 4294967295 Mapper.max-lowq-ratio: 4294967295 Mapper.max-seed-chains: 511 Mapper.max-seed-freq: 16 Mapper.max-splice-gap: 150 Mapper.max-splice-olap: 16 Mapper.min-intron-bases: 20 Mapper.n-base-qual: 2 Mapper.read-edge-seeds: 0 Mapper.reduce-seed-ext: 0 Mapper.rna-filt-ratio: 25 Mapper.rna-max-covg-gap: 150 Mapper.rna-max-recurs: 65536 Mapper.rna-span-log-min: 13 Mapper.seed-density: 0.5 Mapper.seed-max-age: 31 Mapper.seed-old-age: 9 Mapper.splice-olap-adj: 4 Mapper.stats-source-sel: 0 Mapper.trace-mode: 0 Mapper.trace-offset: 0 Mapper.trace-read-id: 0 append-read-index-to-name: false assert-valid-cigar: false bam2dbam-threads: 12 bin-split-target-size: 104857600 bin-split-threshold: 7158278826 binner-use-odirect: true bqsr-context-low-quality-tail: 2 bqsr-cycle-indel-context: 3 bqsr-cycle-mismatch-context: 2 bqsr-emit-indel-tags: true bqsr-enable-recal-indels: true bqsr-match-gatk: true bqsr-max-cycle-value: 500 c2s_aligner_packet_size: 524288 c2s_aligner_pool_size: 64 c2s_decomp_packet_size: 1048576 c2s_decomp_pool_size: 64 c2s_graph_packet_size: 65536 c2s_graph_pool_size: 256 c2s_hmm_packet_size: 4096 c2s_hmm_pool_size: 128 c2s_smw_packet_size: 4096 c2s_smw_pool_size: 128 cgvcf-num-file-scan-threads: 8 cgvcf-save-tmp-files: false cgvcf-split-chromosomes: false cnv-combined-counts: resource_bundle/cnv/TSO500_DRAGEN_BASELINE_SOLID_matched_targets_v2.combined.counts.txt.gz cnv-count-mapq-zero: false cnv-enable-gcbias-correction: false cnv-enable-ref-calls: true cnv-enable-split-intervals: false cnv-filter-copy-ratio: 0 cnv-filter-qual: 0 cnv-linear-regression-noise-removal: true cnv-normalize-counts-by-good-median: true cnv-normalize-rows-by-interval-size: true cnv-segmentation-bed: resource_bundle/cnv/dragen_tso500_manifest_cnv_genes_predefined_cutoff_FFPE.bed cnv-target-bed: resource_bundle/cnv/TSO500_DRAGEN_TARGET_SOLID_matched_targets.bed combine-samples-by-name: false credentials-1:  credentials-2:  credentials-3:  dbam2bam_threads: 32 debug: 0 disable_reg_validation: 0 distinct-dbam-input-format: true dump-hang-diag-first: true dump-map-align-registers: 0 dump_config: 0 dump_registers: 0 dupmark-version: hash echo_aligner_log: 0 echo_general_log: 0 echo_mapper_log: 0 enable-auto-multifile: true enable-bam-indexing: true enable-bqsr: false enable-cnv: true enable-deterministic-sort: true enable-duplicate-marking: false enable-gis: false enable-hang-diag: true enable-hla: false enable-http-server: false enable-map-align: true enable-map-align-output: true enable-methylation-calling: true enable-positional-collapsing: false enable-pstack: true enable-public-bitstream: false enable-rna-quantification: false enable-sampling: true enable-single-cell-rna: false enable-sort: true enable-spin: false enable-umi-stat-estimator: false enable-variant-caller: true enable-variant-deduplication: false enable-vcf-indexing: true enable-watchdog: true enable-write-input-dbam: false events-log-file: events.csv evict_all_intermediate_results: false fastq-n-quality: 2 fastq-offset: 33 fastq2dbam_ratio: 2 fastq_block_size: 1048576 fastq_pool_size: 4 fastqc-adapter-file: adapter_sequences.fasta fastqc-granularity: 7 fastqc-only: false filter-flags-from-output: 0 force:  gc-metrics-cover-percent: 75 gc-metrics-enable: true gc-metrics-num-bins: 5 gc-metrics-only-covered: false gc-metrics-window-size: 100 generate-en-tags: false generate-md-tags: false generate-sa-tags: true generate-xq-tags: true generate-zs-tags: false gis-annotate-tso-bed-in:  gis-annotate-tso-cnv: false gis-annotate-tso-cnv-in:  gis-annotate-tso-genes: false gis-genome-abcn: false gis-hmm-Z: 19 gis-input-dialect: bam gis-input-list:  gis-is-tumor: true gis-max-noise-frac: 0.03 gis-min-align-quality: 30 gis-min-coverage-hrd: 1 gis-min-coverage-snp: 40 gis-min-coverage-tso: 1 gis-min-phred-score: 30 gis-nev: 15 gis-pon: /opt/dragen/3.11.2/resources/PhenoHRD/pon.json.gz gis-print-lb: true gis-print-lr: true gis-print-vaf: true gis-probes: /opt/dragen/3.11.2/resources/PhenoHRD/Probes.vcf.gz gis-qc-maxBAlleleNoise: 0.08 gis-qc-maxBAlleleRatio: 0.85 gis-qc-min50x: 50 gis-qc-mode: illumina gis-threads: 8 hla-allele-frequency-file: hla_classI_allele_frequency.csv hla-reference-file: hla_classI_ref_freq.fasta hla-unmapped: false ht-anchor-bin-bits: 0 ht-cost-coeff-seed-freq: 0.5 ht-cost-coeff-seed-len: 1 ht-cost-penalty: 0 ht-cost-penalty-incr: 0.69999999999999996 ht-crc-extended: 0 ht-crc-primary: 0 ht-dump-int-params: 0 ht-ext-rec-cost: 4 ht-ext-table-alloc: 0 ht-max-dec-factor: 1 ht-max-ext-incr: 12 ht-max-ext-seed-len: 0 ht-max-seed-freq: 16 ht-max-seed-freq-len: 98 ht-max-table-chunks: 0 ht-mem-limit: 0GB ht-methylated: false ht-methylated-combined: false ht-min-repair-prob: 0.20000000000000001 ht-override-size-check: 0 ht-pri-max-seed-freq: 0 ht-rand-hit-extend: 8 ht-rand-hit-hifreq: 1 ht-ref-seed-interval: 1 ht-repair-strategy: 0 ht-seed-len: 21 ht-size: 0GB ht-soft-seed-freq-cap: 12 ht-target-seed-freq: 4 ht-test-only: 0 ht-write-hash-bin: 0 http-server-port: 7993 ignore-version-check: false input-qname-suffix-delimiter: / linkedreads-correction-table1: linkedreads_corrections_1.txt linkedreads-correction-table2: linkedreads_corrections_2.txt linkedreads-correction-table3: linkedreads_corrections_3.txt linkedreads-enable: false logfile_prefix: /opt/edico/logs/ logging-to-output-dir: true mapper_cigar: 0 max_bin_size: 943718400 max_ios_inflight: 1024 methylation-TAPS: false methylation-compress-cx-report: false methylation-generate-cytosine-report: false methylation-generate-mbias-report: false methylation-keep-ref-cytosine: false methylation-mapping-implementation: single-pass methylation-match-bismark: false methylation-protocol: none methylation-reports-only: false min-predicted-output-gb: 200 msi-command: tumor-only msi-coverage-threshold: 60 msi-distance-threshold: 0.100000001 msi-microsatellites-file: resource_bundle/msi/references/microsatellites-TSO500-SOLID-concordant.list msi-ref-normal-dir: resource_bundle/msi/data/TSO500-Solid multiplier: 1 no-reset: false output-directory: DnaDragenCaller output-file-prefix: TVD0016-D01-P01-A00 output-format: bam pair-by-name: true pair-suffix-delimiter: / partition-on-compression-bottleneck: false pe-stats-continuous-update: false pe-stats-interval-delay: 5 pe-stats-interval-memory: 10 pe-stats-interval-size: 25000 pe-stats-sample-size: 100000 pe-stats-update-log-only: false preserve-bqsr-tags: false preserve-map-align-order: false qc-contam-min-basequal: 30 qc-contam-min-mapq: 30 qc-coverage-ignore-overlaps: true qc-coverage-region-1: resource_bundle/small_variants/TST500C_CodingRegions_hg19.bed qc-coverage-region-2: resource_bundle/small_variants/TST500C_manifest.exon.bed qc-coverage-reports-1: callability  qc-coverage-reports-2: cov_report  qc-coverage-tag-1: tmb qc-coverage-tag-2: exon qc-indel-denovo-quality-threshold: 0.02 qc-snp-denovo-quality-threshold: 0.050000000000000003 read-trimmers: none recordset-memory: 1073741824 ref-dir: hashtable reg_errors_are_warnings: 0 repeat-genotype-enable: false repeat-genotype-min-anchor-mapq: 60 repeat-genotype-min-baseq: 20 repeat-genotype-min-score: 0.90000000000000002 repeat-genotype-read-depth: 0 repeat-genotype-read-length: 0 repeat-genotype-region-extension-length: 1000 repeat-genotype-skip-unaligned: true repeat-genotype-specs:  rna-ann-sj-min-len: 6 rna-cv-min-expression: 0 rna-gf-aggressive-filters: false rna-gf-allow-overlapping-genes: false rna-gf-avg-mapq-threshold-div: 256 rna-gf-blast-pairs:  rna-gf-coverage-lookup-window: 1000 rna-gf-enable-read-share-cleanup: false rna-gf-enriched-genes:  rna-gf-enriched-only: true rna-gf-enriched-regions:  rna-gf-exon-snap: 50 rna-gf-filter-chrm: false rna-gf-mate-overhang: 8 rna-gf-max-partners: 3 rna-gf-merge-calls: true rna-gf-min-alt-to-ref: 0.00999999978 rna-gf-min-anchor: 12 rna-gf-min-blast-pairs-eval: 1e-100 rna-gf-min-breakpoint-distance: 0 rna-gf-min-breakpoint-mapq: 20 rna-gf-min-cis-distance: 200000 rna-gf-min-covered-bases: 125 rna-gf-min-covered-bases-uncaptured: 79 rna-gf-min-neighbor-dist: 15 rna-gf-min-nonref-split-support: 3 rna-gf-min-score: 0.5 rna-gf-min-score-ratio: 0.150000006 rna-gf-min-support: 2 rna-gf-min-support-be: 10 rna-gf-min-unique-alignments: 2 rna-gf-num-threads: 4 rna-gf-ref-anchor: 8 rna-gf-report-antisense: false rna-gf-report-intergenic: false rna-gf-report-intronic: false rna-gf-restrict-genes: true rna-gf-score-model:  rna-gf-split-percent-align: 0.00100000005 rna-library-type: A rna-mapq-unique: 0 rna-quantification-fld-max: 1000 rna-quantification-fld-mean: 250 rna-quantification-fld-sd: 25 rna-quantification-full-concordance: false rna-quantification-gc-bias: true rna-quantification-inference-max: 10000 rna-quantification-inference-min: 100 rna-quantification-init-uniform: 0 rna-quantification-tlen-min: 500 rna-quantification-use-em: 0 rna-repeat-genes:  rna-repeat-intervals:  rna-sjs-max-size: 1000000000 rna_aligner_buffer_size: 67108864 rna_aligner_buffers: 0 rrna-filter-enable: false rrna-filter-mode: 3 rrna-filter-score-bonus-coeff: 0.025000000000000001 rrna-filter-score-bonus-const: 2 s2c_dbam_block_size: 65536 s2c_dbam_pool_size: 32 s2c_decomp_block_size: 262144 s2c_decomp_pool_size: 64 s2c_graph_block_size: 16384 s2c_graph_pool_size: 256 s2c_hmm_block_size: 16384 s2c_hmm_pool_size: 16384 s2c_phase1_packet_size: 16384 s2c_phase2_packet_size: 16384 s2c_smw_block_size: 16384 s2c_smw_pool_size: 2048 scrna-count-introns: false scrna-global-umi: false single-cell-number-cells: 3000 single-cell-number-threads: 48 single-cell-threshold: ratio soft-read-trimmers: polyg sort_buffer_size: 1048576 stop-at-read: 0 strip-input-qname-suffixes: true sv-denovo-threshold: 20 sv-enable-rrm-for-insertions-in-cancer-calling-modes: true sv-enable-rrm-for-insertions-in-germline-calling-modes: true sv-filtered-contigs: *_random chrUn_* *_alt HLA-* GL*  sv-min-diploid-variant-score: 10 sv-min-pass-diploid-gt-score: 5 sv-min-pass-diploid-variant-score: 20 sv-min-pass-somatic-score: 30 sv-min-somatic-score: 10 sv-report-small-dup-as-ins: true trim-disable-mapping: false trim-filter-dummy-len: 10 trim-filter-set-flag: true trim-min-len-read1: 20 trim-min-len-read2: 20 trim-min-length: 20 trim-polyg-early-exit-threshold: -500 trim-polyg-g-score-r1-3prime: 15 trim-polyg-g-score-r1-5prime: 0 trim-polyg-g-score-r2-3prime: 15 trim-polyg-g-score-r2-5prime: 0 trim-polyg-kmer-len: 25 trim-polyg-kmer-non-g: 2 trim-polyg-min-trim-r1-3prime: 6 trim-polyg-min-trim-r1-5prime: 6 trim-polyg-min-trim-r2-3prime: 6 trim-polyg-min-trim-r2-5prime: 6 tso500-cnv-enable-low-validation-filter: false tso500-contam-vcf: resource_bundle/contamination/Contamination.vcf tso500-solid-cnv: true tso500-solid-msi: true tso500-solid-snv: true tso500-solid-umi: true tso500-use-combined-license: true tumor-fastq-list: TVD0016-D01-P01-A00.fastq_list.csv tumor-fastq-list-sample-id: TVD0016-D01-P01-A00 umi-base-representation-min-ratio: 0.5 umi-correction-scheme: lookup umi-emit-multiplicity: both umi-enable: true umi-enable-contextual-corrections: true umi-enable-probability-model-merging: false umi-enable-shift-corrections: true umi-enable-trimming: true umi-end-mask-length: 3 umi-generate-bam-tags: true umi-generate-error-rate-bam-tags: false umi-masked-base-qual: 1 umi-max-base-quality: 63 umi-max-collision-rate: 1000 umi-max-read-error-rate: 1 umi-mem-throttle-gb: 30 umi-metrics-interval-file: resource_bundle/small_variants/TSO_HRD_manifest_randomized.bed umi-min-consensus-base-quality: 0 umi-min-input-base-quality: 0 umi-min-map-quality: 0 umi-min-reads-per-region: 4096 umi-min-supporting-reads: 1 umi-padding: A umi-preserve-input-tags: false umi-probability-merging-duplex-merging-thres: 1 umi-probability-merging-max-transition-ratio: 100000000 umi-probability-merging-min-isize-freq: 0.001 umi-probability-merging-seq-error: 0.001 umi-probability-merging-simplex-fuzzy-merging-thres: 1 umi-probability-merging-simplex-merging-thres: 1 umi-r1-length: 0 umi-random-merge-factor: 2 umi-read-minority-min-ratio: 0.5 umi-soft-clip-ratio: 0.5 umi-source: qname umi-start-mask-length: 1 umi-stat-estimation-max-fragment-count: 10 umi-stat-estimation-max-fragment-size: 1000 umi-stat-estimation-max-interval-number: 10 umi-stat-estimation-min-probability-unique-fragment: 0.998 umi-stat-estimation-umi-jumping-estimation-method: simplex umi-trim-allowed-mismatches: 1 umi-verbose-metrics: false use-mock-config: false vc-active-only: false vc-blacklist-bed: resource_bundle/small_variants/pepe_blacklist_sorted.bed vc-callability-tumor-thresh: 50 vc-columnwise-base-qual-threshold: 30 vc-combine-phased-variants-distance: 15 vc-decoy-contigs: NC_007605 hs37d5 chrUn_KN707*v1_decoy chrUn_JTFH0100*v1_decoy KN707*.1 JTFH0100*.1 chrEBV CMV HBV HCV* HIV* KSHV HTLV* MCV SV40 HPV*  vc-depth-annotation-threshold: 100 vc-emit-ref-confidence: BP_RESOLUTION vc-emit-zero-coverage-intervals: true vc-enable-basecall-filter: false vc-enable-deterministic-run: true vc-enable-hw-hmm: true vc-enable-hw-hmm-dump-receiver-data: false vc-enable-hw-hmm-dump-sender-data: false vc-enable-hw-hmm-dump-worker-data: false vc-enable-hw-smw: true vc-enable-hw-smw-dump-receiver-data: false vc-enable-hw-smw-dump-sender-data: false vc-enable-hw-smw-dump-worker-data: false vc-enable-mnv-decomposed-vcf: true vc-enable-non-primary-allelic-filter: true vc-enable-realign-soft-clip-reads-only: true vc-enable-triallelic-filter: false vc-enable-umi-solid: true vc-enable-vcf-output: true vc-evidence-bam-clipped-read-threshold: 0 vc-homref-depth-filter-threshold: 100 vc-hotspot-log10-prior-boost: 3 vc-hotspot-systematic-noise-multiplier: 0.150000006 vc-hw-hmm-timeout: 100000 vc-limit-genomecov-output: false vc-max-alternate-alleles: 6 vc-max-haps-per-job: 2 vc-min-base-qual: 30 vc-min-contig-qual: 30 vc-mnv-emit-component-calls: true vc-pcr-del-gop-offset: -1 vc-pcr-ind-gop-offset-per-read-category: true vc-pcr-ins-gop-offset: -1 vc-pcr-tumor-del-gop-offset: 14 vc-pcr-tumor-ins-gop-offset: 14 vc-set-to-N-base-qual: 30 vc-somatic-hotspots: resource_bundle/small_variants/pepe2_prior.vcf vc-sq-call-threshold: -1 vc-sw-cell-width: 16 vc-sw-instruction-set: sse2 vc-sw-mode: 0 vc-systematic-noise: resource_bundle/small_variants/mean_gvcf_bq30_lowSQ_v1.0_systematic_noise_v2.bed.gz vc-target-bed: resource_bundle/small_variants/TST500C_manifest.bed vc-target-bed-padding: 8 vc-use-systematic-noise-in-scoring: true vd-output-match-log: false vqsr-lod-cutoff: -5.0 vqsr-num-gaussians: 8,2,4,2 watchdog-active-timeout: 600 watchdog-dump-processes: true; watchdog-exit-on-hang: true watchdog-freemem-threshold: 2GB watchdog-idle-timeout: 600 watchdog-max-threads: 8388608 watchdog-poll-interval: 1 watchdog-resources-monitored: THREADS IO MEMORY  watchdog-verbose-logging: true num-engines: 5  Aligner.HardClipTags: 1  Aligner.HardClips: 6  Aligner.aln-min-score: 22  Aligner.bed-base-div64: 24571868  Aligner.clip-pe-overhang: 0  Aligner.give-pair-score: 0  Aligner.idx-base-div64: 23827264  Aligner.intr-motif0-pen: 0  Aligner.intr-motif12-pen: 0  Aligner.intr-motif34-pen: 0  Aligner.intr-motif56-pen: 0  Aligner.mapq-coeff-scaled: 38912  Aligner.match-n-score: 31  Aligner.methyl-aln-mode: 0  Aligner.ref-base-div64: 0  Aligner.rrna-bonus-coeff: 0  Aligner.rrna-bonus-const: 0  Aligner.rrna-mode: 0  Aligner.rrna-ref-id: 0  Aligner.seed-len-inv: 195  Aligner.steer-delta: 12  Aligner.stitch-skip-bias: 0  Aligner.supp-min-score-adj: 8  Mapper.adapter-detect-0: 2284439564 0  Mapper.adapter-detect-1: 2809932556 0  Mapper.adapter-detect-10: 0 0  Mapper.adapter-detect-11: 0 0  Mapper.adapter-detect-12: 0 0  Mapper.adapter-detect-13: 0 0  Mapper.adapter-detect-14: 0 0  Mapper.adapter-detect-15: 0 0  Mapper.adapter-detect-2: 3533599244 0  Mapper.adapter-detect-3: 870182156 0  Mapper.adapter-detect-4: 0 0  Mapper.adapter-detect-5: 0 0  Mapper.adapter-detect-6: 0 0  Mapper.adapter-detect-7: 0 0  Mapper.adapter-detect-8: 0 0  Mapper.adapter-detect-9: 0 0  Mapper.adapter-min-trim: 4  Mapper.adapter-trim-r1-3p-s0-p0: 0  Mapper.adapter-trim-r1-3p-s0-p1: 0  Mapper.adapter-trim-r1-3p-s0-p2: 0  Mapper.adapter-trim-r1-3p-s0-p3: 0  Mapper.adapter-trim-r1-3p-s1-p0: 0  Mapper.adapter-trim-r1-3p-s1-p1: 0  Mapper.adapter-trim-r1-3p-s1-p2: 0  Mapper.adapter-trim-r1-3p-s1-p3: 0  Mapper.adapter-trim-r1-3p-s2-p0: 0  Mapper.adapter-trim-r1-3p-s2-p1: 0  Mapper.adapter-trim-r1-3p-s2-p2: 0  Mapper.adapter-trim-r1-3p-s2-p3: 0  Mapper.adapter-trim-r1-3p-s3-p0: 0  Mapper.adapter-trim-r1-3p-s3-p1: 0  Mapper.adapter-trim-r1-3p-s3-p2: 0  Mapper.adapter-trim-r1-3p-s3-p3: 0  Mapper.adapter-trim-r1-3p-s4-p0: 0  Mapper.adapter-trim-r1-3p-s4-p1: 0  Mapper.adapter-trim-r1-3p-s4-p2: 0  Mapper.adapter-trim-r1-3p-s4-p3: 0  Mapper.adapter-trim-r1-3p-s5-p0: 0  Mapper.adapter-trim-r1-3p-s5-p1: 0  Mapper.adapter-trim-r1-3p-s5-p2: 0  Mapper.adapter-trim-r1-3p-s5-p3: 0  Mapper.adapter-trim-r1-3p-s6-p0: 0  Mapper.adapter-trim-r1-3p-s6-p1: 0  Mapper.adapter-trim-r1-3p-s6-p2: 0  Mapper.adapter-trim-r1-3p-s6-p3: 0  Mapper.adapter-trim-r1-3p-s7-p0: 0  Mapper.adapter-trim-r1-3p-s7-p1: 0  Mapper.adapter-trim-r1-3p-s7-p2: 0  Mapper.adapter-trim-r1-3p-s7-p3: 0  Mapper.adapter-trim-r1-5p-s0-p0: 0  Mapper.adapter-trim-r1-5p-s0-p1: 0  Mapper.adapter-trim-r1-5p-s0-p2: 0  Mapper.adapter-trim-r1-5p-s0-p3: 0  Mapper.adapter-trim-r1-5p-s1-p0: 0  Mapper.adapter-trim-r1-5p-s1-p1: 0  Mapper.adapter-trim-r1-5p-s1-p2: 0  Mapper.adapter-trim-r1-5p-s1-p3: 0  Mapper.adapter-trim-r1-5p-s2-p0: 0  Mapper.adapter-trim-r1-5p-s2-p1: 0  Mapper.adapter-trim-r1-5p-s2-p2: 0  Mapper.adapter-trim-r1-5p-s2-p3: 0  Mapper.adapter-trim-r1-5p-s3-p0: 0  Mapper.adapter-trim-r1-5p-s3-p1: 0  Mapper.adapter-trim-r1-5p-s3-p2: 0  Mapper.adapter-trim-r1-5p-s3-p3: 0  Mapper.adapter-trim-r1-5p-s4-p0: 0  Mapper.adapter-trim-r1-5p-s4-p1: 0  Mapper.adapter-trim-r1-5p-s4-p2: 0  Mapper.adapter-trim-r1-5p-s4-p3: 0  Mapper.adapter-trim-r1-5p-s5-p0: 0  Mapper.adapter-trim-r1-5p-s5-p1: 0  Mapper.adapter-trim-r1-5p-s5-p2: 0  Mapper.adapter-trim-r1-5p-s5-p3: 0  Mapper.adapter-trim-r1-5p-s6-p0: 0  Mapper.adapter-trim-r1-5p-s6-p1: 0  Mapper.adapter-trim-r1-5p-s6-p2: 0  Mapper.adapter-trim-r1-5p-s6-p3: 0  Mapper.adapter-trim-r1-5p-s7-p0: 0  Mapper.adapter-trim-r1-5p-s7-p1: 0  Mapper.adapter-trim-r1-5p-s7-p2: 0  Mapper.adapter-trim-r1-5p-s7-p3: 0  Mapper.adapter-trim-r2-3p-s0-p0: 0  Mapper.adapter-trim-r2-3p-s0-p1: 0  Mapper.adapter-trim-r2-3p-s0-p2: 0  Mapper.adapter-trim-r2-3p-s0-p3: 0  Mapper.adapter-trim-r2-3p-s1-p0: 0  Mapper.adapter-trim-r2-3p-s1-p1: 0  Mapper.adapter-trim-r2-3p-s1-p2: 0  Mapper.adapter-trim-r2-3p-s1-p3: 0  Mapper.adapter-trim-r2-3p-s2-p0: 0  Mapper.adapter-trim-r2-3p-s2-p1: 0  Mapper.adapter-trim-r2-3p-s2-p2: 0  Mapper.adapter-trim-r2-3p-s2-p3: 0  Mapper.adapter-trim-r2-3p-s3-p0: 0  Mapper.adapter-trim-r2-3p-s3-p1: 0  Mapper.adapter-trim-r2-3p-s3-p2: 0  Mapper.adapter-trim-r2-3p-s3-p3: 0  Mapper.adapter-trim-r2-3p-s4-p0: 0  Mapper.adapter-trim-r2-3p-s4-p1: 0  Mapper.adapter-trim-r2-3p-s4-p2: 0  Mapper.adapter-trim-r2-3p-s4-p3: 0  Mapper.adapter-trim-r2-3p-s5-p0: 0  Mapper.adapter-trim-r2-3p-s5-p1: 0  Mapper.adapter-trim-r2-3p-s5-p2: 0  Mapper.adapter-trim-r2-3p-s5-p3: 0  Mapper.adapter-trim-r2-3p-s6-p0: 0  Mapper.adapter-trim-r2-3p-s6-p1: 0  Mapper.adapter-trim-r2-3p-s6-p2: 0  Mapper.adapter-trim-r2-3p-s6-p3: 0  Mapper.adapter-trim-r2-3p-s7-p0: 0  Mapper.adapter-trim-r2-3p-s7-p1: 0  Mapper.adapter-trim-r2-3p-s7-p2: 0  Mapper.adapter-trim-r2-3p-s7-p3: 0  Mapper.adapter-trim-r2-5p-s0-p0: 0  Mapper.adapter-trim-r2-5p-s0-p1: 0  Mapper.adapter-trim-r2-5p-s0-p2: 0  Mapper.adapter-trim-r2-5p-s0-p3: 0  Mapper.adapter-trim-r2-5p-s1-p0: 0  Mapper.adapter-trim-r2-5p-s1-p1: 0  Mapper.adapter-trim-r2-5p-s1-p2: 0  Mapper.adapter-trim-r2-5p-s1-p3: 0  Mapper.adapter-trim-r2-5p-s2-p0: 0  Mapper.adapter-trim-r2-5p-s2-p1: 0  Mapper.adapter-trim-r2-5p-s2-p2: 0  Mapper.adapter-trim-r2-5p-s2-p3: 0  Mapper.adapter-trim-r2-5p-s3-p0: 0  Mapper.adapter-trim-r2-5p-s3-p1: 0  Mapper.adapter-trim-r2-5p-s3-p2: 0  Mapper.adapter-trim-r2-5p-s3-p3: 0  Mapper.adapter-trim-r2-5p-s4-p0: 0  Mapper.adapter-trim-r2-5p-s4-p1: 0  Mapper.adapter-trim-r2-5p-s4-p2: 0  Mapper.adapter-trim-r2-5p-s4-p3: 0  Mapper.adapter-trim-r2-5p-s5-p0: 0  Mapper.adapter-trim-r2-5p-s5-p1: 0  Mapper.adapter-trim-r2-5p-s5-p2: 0  Mapper.adapter-trim-r2-5p-s5-p3: 0  Mapper.adapter-trim-r2-5p-s6-p0: 0  Mapper.adapter-trim-r2-5p-s6-p1: 0  Mapper.adapter-trim-r2-5p-s6-p2: 0  Mapper.adapter-trim-r2-5p-s6-p3: 0  Mapper.adapter-trim-r2-5p-s7-p0: 0  Mapper.adapter-trim-r2-5p-s7-p1: 0  Mapper.adapter-trim-r2-5p-s7-p2: 0  Mapper.adapter-trim-r2-5p-s7-p3: 0  Mapper.alt-aware: 0  Mapper.chain-filt-ratio: 1024  Mapper.pri-crc-poly: 2C991CE6A8DD55  Mapper.sec-crc-poly: 1524CA66E8D39  Mapper.cut-bases: 0  Mapper.edit-pattern: 1  Mapper.edit-period: 15  Mapper.edit-seeds-limit: 6  Mapper.enable-anchors: 0  Mapper.enable-ann-sjs: 0  Mapper.extab-base-div64: 477556700  Mapper.filter-dummy-len: 10  Mapper.max-read-len: 4294967295  Mapper.methyl-map-mode: 0  Mapper.min-read-len: 0  Mapper.min-trim-bases: 0  Mapper.polyg-early-exit: 4294966796  Mapper.polyg-g-score: 251662080  Mapper.polyg-kmer-len: 25  Mapper.polyg-kmer-non-g: 2  Mapper.polyg-min-trim: 101058054  Mapper.pos-bin-gran-sel: 7  Mapper.pri-crc-bits: 54  Mapper.pri-seed-bases: 21  Mapper.qual-cutoff: 4294967295  Mapper.ref-alt-seed: 3049725952  Mapper.ref-seed-interval: 16  Mapper.rna-mode: 0  Mapper.sec-crc-bits: 49  Mapper.seed-pattern: 1  Mapper.seed-period: 2  Mapper.sjs-base-div64: 529785048  Mapper.table-base-div64: 24571868  Mapper.table-size-64ths: 54  Mapper.trim-flags: 256  Mapper.trim-steps: 4294967281  Mapper.trim-steps-soft: 2 

• file path for RNA alignments: Logs_Intermediates/RnaDragenCaller/<sample_ID>/<sample_ID>.bam

@HD	VN:1.4	SO:coordinate
@SQ	SN:chr1	LN:249250621
@SQ	SN:chr2	LN:243199373
@SQ	SN:chr3	LN:198022430
@SQ	SN:chr4	LN:191154276
@SQ	SN:chr5	LN:180915260
@SQ	SN:chr6	LN:171115067
@SQ	SN:chr7	LN:159138663
@SQ	SN:chr8	LN:146364022
@SQ	SN:chr9	LN:141213431
@SQ	SN:chr10	LN:135534747
@SQ	SN:chr11	LN:135006516
@SQ	SN:chr12	LN:133851895
@SQ	SN:chr13	LN:115169878
@SQ	SN:chr14	LN:107349540
@SQ	SN:chr15	LN:102531392
@SQ	SN:chr16	LN:90354753
@SQ	SN:chr17	LN:81195210
@SQ	SN:chr18	LN:78077248
@SQ	SN:chr19	LN:59128983
@SQ	SN:chr20	LN:63025520
@SQ	SN:chr21	LN:48129895
@SQ	SN:chr22	LN:51304566
@SQ	SN:chrX	LN:155270560
@SQ	SN:chrY	LN:59373566
@SQ	SN:chrM	LN:16569
@SQ	SN:GL000207.1	LN:4262
@SQ	SN:GL000226.1	LN:15008
@SQ	SN:GL000229.1	LN:19913
@SQ	SN:GL000231.1	LN:27386
@SQ	SN:GL000210.1	LN:27682
@SQ	SN:GL000239.1	LN:33824
@SQ	SN:GL000235.1	LN:34474
@SQ	SN:GL000201.1	LN:36148
@SQ	SN:GL000247.1	LN:36422
@SQ	SN:GL000245.1	LN:36651
@SQ	SN:GL000197.1	LN:37175
@SQ	SN:GL000203.1	LN:37498
@SQ	SN:GL000246.1	LN:38154
@SQ	SN:GL000249.1	LN:38502
@SQ	SN:GL000196.1	LN:38914
@SQ	SN:GL000248.1	LN:39786
@SQ	SN:GL000244.1	LN:39929
@SQ	SN:GL000238.1	LN:39939
@SQ	SN:GL000202.1	LN:40103
@SQ	SN:GL000234.1	LN:40531
@SQ	SN:GL000232.1	LN:40652
@SQ	SN:GL000206.1	LN:41001
@SQ	SN:GL000240.1	LN:41933
@SQ	SN:GL000236.1	LN:41934
@SQ	SN:GL000241.1	LN:42152
@SQ	SN:GL000243.1	LN:43341
@SQ	SN:GL000242.1	LN:43523
@SQ	SN:GL000230.1	LN:43691
@SQ	SN:GL000237.1	LN:45867
@SQ	SN:GL000233.1	LN:45941
@SQ	SN:GL000204.1	LN:81310
@SQ	SN:GL000198.1	LN:90085
@SQ	SN:GL000208.1	LN:92689
@SQ	SN:GL000191.1	LN:106433
@SQ	SN:GL000227.1	LN:128374
@SQ	SN:GL000228.1	LN:129120
@SQ	SN:GL000214.1	LN:137718
@SQ	SN:GL000221.1	LN:155397
@SQ	SN:GL000209.1	LN:159169
@SQ	SN:GL000218.1	LN:161147
@SQ	SN:GL000220.1	LN:161802
@SQ	SN:GL000213.1	LN:164239
@SQ	SN:GL000211.1	LN:166566
@SQ	SN:GL000199.1	LN:169874
@SQ	SN:GL000217.1	LN:172149
@SQ	SN:GL000216.1	LN:172294
@SQ	SN:GL000215.1	LN:172545
@SQ	SN:GL000205.1	LN:174588
@SQ	SN:GL000219.1	LN:179198
@SQ	SN:GL000224.1	LN:179693
@SQ	SN:GL000223.1	LN:180455
@SQ	SN:GL000195.1	LN:182896
@SQ	SN:GL000212.1	LN:186858
@SQ	SN:GL000222.1	LN:186861
@SQ	SN:GL000200.1	LN:187035
@SQ	SN:GL000193.1	LN:189789
@SQ	SN:GL000194.1	LN:191469
@SQ	SN:GL000225.1	LN:211173
@SQ	SN:GL000192.1	LN:547496
@SQ	SN:NC_007605	LN:171823
@SQ	SN:hs37d5	LN:35477943
@RG	ID:1	LB:TVR0014-R03-P01-A00	PU:1	SM:TVR0014-R03-P01-A00
@RG	ID:2	LB:TVR0014-R03-P01-A00	PU:2	SM:TVR0014-R03-P01-A00
@RG	ID:3	LB:TVR0014-R03-P01-A00	PU:3	SM:TVR0014-R03-P01-A00
@RG	ID:4	LB:TVR0014-R03-P01-A00	PU:4	SM:TVR0014-R03-P01-A00
@PG	ID: Hash Table Build	VN: 01.003.044.3.11.2-hv-8	CL: /opt/dragen/3.11.2/bin/dragen --build-hash-table true --output-directory /staging/illumina/DRAGEN_TSO500_2.6.2/ref_hashtable --ht-reference /staging/illumina/DRAGEN_TSO500_2.6.2/ref_hashtable/genome.fa --ht-num-threads 48 --ht-build-rna-hashtable true --enable-cnv true	DS: digest_type: 1 digest: 0x6C40717F ref_digest: 0xC2311E75 ref_index_digest: 0xB4307AF0 hash_digest: 0x8E6AAC7D
@PG	ID: DRAGEN HW build	VN: 18101306
@CO	TS:Fri Mar 20 13:15:48 2026
@CO	LC:eaba06df31957562380df7521
@PG	ID: DRAGEN SW build	VN: 07.021.624.3.11.2	CL: /opt/edico/bin/dragen --output-directory RnaDragenCaller --output-file-prefix TVR0014-R03-P01-A00 --tso500-solid-rna true --ref-load-hash-bin true --ref-dir hashtable --annotation-file resource_bundle/dragen/gencode.v19.annotation_filtered_20160301.gtf --rna-gf-blast-pairs resource_bundle/dragen/hg19_unassigned_TSO500.cdsplus.fa.allvsall.outfmt6.genesym.gz --rna-gf-enriched-genes resource_bundle/dragen/TST170_RNAgenes_v2.txt --rna-repeat-intervals resource_bundle/dragen/rna_repeats_hg19.bed --fastq-list TVR0014-R03-P01-A00.fastq_list.csv --fastq-list-sample-id TVR0014-R03-P01-A00 --qc-coverage-region-1 resource_bundle/dragen/MixRNA_Manifest.bed --qc-coverage-region-2 resource_bundle/dragen/MixRNA_Manifest.bed --qc-coverage-filters-1 countduplicate --qc-coverage-tag-1 duped --qc-coverage-tag-2 deduped --qc-coverage-region-3 resource_bundle/qcresources/MixRNA_Manifest.exon.bed --qc-coverage-tag-3 exon --qc-coverage-reports-3 cov_report --qc-coverage-ignore-overlaps true --events-log-file events.csv --tso500-use-combined-license true --logging-to-output-dir true --force	DS: Aligner.align-direction: 4 Aligner.aln-en-mask: 15 Aligner.aln-enable: 1 Aligner.backtrace-delay: 8 Aligner.bed-score-bonus: 11 Aligner.chicken: 0 Aligner.dedup-min-qual: 15 Aligner.disable-lfsr: 0 Aligner.en-alt-hap-aln: 1 Aligner.en-chimeric-aln: 1 Aligner.exon-jump-en: 1 Aligner.filt-clip1-pair: 10 Aligner.filt-clip1-unpr: -5 Aligner.filt-clip2-pair: 5 Aligner.filt-clip2-unpr: -10 Aligner.filt-min-qual: 0 Aligner.fix-overlap-mapq: 0 Aligner.gap-ext-pen: 1 Aligner.gap-open-pen: 6 Aligner.global: 0 Aligner.hard-clip-tags: 1 Aligner.hard-clips: 6 Aligner.hw-mapq-max: 250 Aligner.leftalign-mode: 2 Aligner.mapq-coeff: 152 Aligner.mapq-floor-1snp: 0 Aligner.mapq-max: 60 Aligner.mapq-min-len: 50 Aligner.mapq-strict-sjs: 0 Aligner.match-score: 1 Aligner.max-rescues: 1023 Aligner.max-stitch-olap: 48 Aligner.min-overhang: 6 Aligner.min-overhang-ann: 4 Aligner.min-score-coeff: 0.0 Aligner.mismatch-pen: 4 Aligner.no-align-score: -8388608 Aligner.no-ambig-strand: 0 Aligner.no-noncan-motifs: 1 Aligner.no-unclip-score: 1 Aligner.no-unpaired: 0 Aligner.paired-mate-info: 1 Aligner.pe-max-penalty: 255 Aligner.pe-orientation: 0 Aligner.pe-sample-max-insert: 65535 Aligner.resc-ifpair-len: 48 Aligner.resc-nopair-len: 0 Aligner.rescue-ceil-factor: 3 Aligner.rescue-hifreq: 0 Aligner.rescue-kmer-len: 32 Aligner.rescue-max-snps: 7 Aligner.rna-max-insert: 4000000 Aligner.rna-pair-pen-rat: 5.71875 Aligner.sample-mapq0: 1 Aligner.sec-aligns: 9 Aligner.sec-aligns-hard: 1 Aligner.sec-phred-delta: 0 Aligner.sec-score-delta: 0 Aligner.supp-aligns: 3 Aligner.supp-as-sec: 0 Aligner.sw-all: 0 Aligner.sw-burst-diffs: 1 Aligner.sw-early-max: 256 Aligner.sw-extra-intvl: 1 Aligner.unclip-score: 5 Aligner.unpaired-pen: 80 Aligner.xs-pair-penalty: 25 Mapper.ann-sj-max-indel: 10 Mapper.chain-diam-lim: 8 Mapper.chain-rad-lim: 5 Mapper.dark-base: 2 Mapper.edit-chain-limit: 29 Mapper.edit-mode: 0 Mapper.edit-read-len: 100 Mapper.edit-seed-num: 6 Mapper.filt-good-qual: 0 Mapper.filter-len-ratio: 4 Mapper.intvl-max-hits: 16 Mapper.intvl-min-chains: 8 Mapper.intvl-sample-hits: 16 Mapper.intvl-seed-length: 60 Mapper.intvl-seed-longer: 8 Mapper.intvl-target-hits: 32 Mapper.map-orientations: 0 Mapper.max-dram-reqs: 0 Mapper.max-hifreq-hits: 16 Mapper.max-intron-bases: 200000 Mapper.max-lowq-bases: 4294967295 Mapper.max-lowq-ratio: 4294967295 Mapper.max-seed-chains: 511 Mapper.max-seed-freq: 32 Mapper.max-splice-gap: 150 Mapper.max-splice-olap: 16 Mapper.min-intron-bases: 20 Mapper.n-base-qual: 2 Mapper.read-edge-seeds: 0 Mapper.reduce-seed-ext: 1 Mapper.rna-filt-ratio: 25 Mapper.rna-max-covg-gap: 150 Mapper.rna-max-recurs: 65536 Mapper.rna-span-log-min: 13 Mapper.seed-density: 0.5 Mapper.seed-max-age: 31 Mapper.seed-old-age: 9 Mapper.splice-olap-adj: 4 Mapper.stats-source-sel: 0 Mapper.trace-mode: 0 Mapper.trace-offset: 0 Mapper.trace-read-id: 0 annotation-file: resource_bundle/dragen/gencode.v19.annotation_filtered_20160301.gtf append-read-index-to-name: false assert-valid-cigar: false bam2dbam-threads: 12 bin-split-target-size: 104857600 bin-split-threshold: 7158278826 binner-use-odirect: true bqsr-context-low-quality-tail: 2 bqsr-cycle-indel-context: 3 bqsr-cycle-mismatch-context: 2 bqsr-emit-indel-tags: true bqsr-enable-recal-indels: true bqsr-match-gatk: true bqsr-max-cycle-value: 500 c2s_aligner_packet_size: 524288 c2s_aligner_pool_size: 64 c2s_decomp_packet_size: 1048576 c2s_decomp_pool_size: 64 c2s_graph_packet_size: 65536 c2s_graph_pool_size: 256 c2s_hmm_packet_size: 4096 c2s_hmm_pool_size: 128 c2s_smw_packet_size: 4096 c2s_smw_pool_size: 128 cgvcf-num-file-scan-threads: 8 cgvcf-save-tmp-files: false cgvcf-split-chromosomes: false combine-samples-by-name: false credentials-1:  credentials-2:  credentials-3:  dbam2bam_threads: 32 debug: 0 disable_reg_validation: 0 distinct-dbam-input-format: true dump-hang-diag-first: true dump-map-align-registers: 0 dump_config: 0 dump_registers: 0 dupmark-version: hash echo_aligner_log: 0 echo_general_log: 0 echo_mapper_log: 0 enable-auto-multifile: true enable-bqsr: false enable-deterministic-sort: true enable-duplicate-marking: true enable-gis: false enable-hang-diag: true enable-hla: false enable-http-server: false enable-map-align: true enable-methylation-calling: true enable-positional-collapsing: false enable-pstack: true enable-public-bitstream: false enable-rna: true enable-rna-gene-fusion: true enable-rna-quantification: true enable-sampling: true enable-single-cell-rna: false enable-sort: true enable-spin: false enable-umi-stat-estimator: false enable-variant-caller: false enable-variant-deduplication: false enable-vcf-indexing: true enable-watchdog: true enable-write-input-dbam: false events-log-file: events.csv evict_all_intermediate_results: false fastq-list: TVR0014-R03-P01-A00.fastq_list.csv fastq-list-sample-id: TVR0014-R03-P01-A00 fastq-n-quality: 2 fastq-offset: 33 fastq2dbam_ratio: 2 fastq_block_size: 1048576 fastq_pool_size: 4 fastqc-adapter-file: adapter_sequences.fasta fastqc-granularity: 7 fastqc-only: false filter-flags-from-output: 0 force:  gc-metrics-cover-percent: 75 gc-metrics-enable: false gc-metrics-num-bins: 5 gc-metrics-only-covered: false gc-metrics-window-size: 100 generate-en-tags: false generate-md-tags: false generate-xq-tags: true generate-zs-tags: false gis-annotate-tso-bed-in:  gis-annotate-tso-cnv: false gis-annotate-tso-cnv-in:  gis-annotate-tso-genes: false gis-genome-abcn: false gis-hmm-Z: 19 gis-input-dialect: bam gis-input-list:  gis-is-tumor: true gis-max-noise-frac: 0.03 gis-min-align-quality: 30 gis-min-coverage-hrd: 1 gis-min-coverage-snp: 40 gis-min-coverage-tso: 1 gis-min-phred-score: 30 gis-nev: 15 gis-pon: /opt/dragen/3.11.2/resources/PhenoHRD/pon.json.gz gis-print-lb: true gis-print-lr: true gis-print-vaf: true gis-probes: /opt/dragen/3.11.2/resources/PhenoHRD/Probes.vcf.gz gis-qc-maxBAlleleNoise: 0.08 gis-qc-maxBAlleleRatio: 0.85 gis-qc-min50x: 50 gis-qc-mode: illumina gis-threads: 8 hla-allele-frequency-file: hla_classI_allele_frequency.csv hla-reference-file: hla_classI_ref_freq.fasta hla-unmapped: false ht-anchor-bin-bits: 0 ht-cost-coeff-seed-freq: 0.5 ht-cost-coeff-seed-len: 1 ht-cost-penalty: 0 ht-cost-penalty-incr: 0.69999999999999996 ht-crc-extended: 0 ht-crc-primary: 0 ht-dump-int-params: 0 ht-ext-rec-cost: 4 ht-ext-table-alloc: 0 ht-max-dec-factor: 1 ht-max-ext-incr: 12 ht-max-ext-seed-len: 0 ht-max-seed-freq: 16 ht-max-seed-freq-len: 98 ht-max-table-chunks: 0 ht-mem-limit: 0GB ht-methylated: false ht-methylated-combined: false ht-min-repair-prob: 0.20000000000000001 ht-override-size-check: 0 ht-pri-max-seed-freq: 0 ht-rand-hit-extend: 8 ht-rand-hit-hifreq: 1 ht-ref-seed-interval: 1 ht-repair-strategy: 0 ht-seed-len: 21 ht-size: 0GB ht-soft-seed-freq-cap: 12 ht-target-seed-freq: 4 ht-test-only: 0 ht-write-hash-bin: 0 http-server-port: 7993 ignore-version-check: false input-qname-suffix-delimiter: / linkedreads-correction-table1: linkedreads_corrections_1.txt linkedreads-correction-table2: linkedreads_corrections_2.txt linkedreads-correction-table3: linkedreads_corrections_3.txt linkedreads-enable: false logfile_prefix: /opt/edico/logs/ logging-to-output-dir: true mapper_cigar: 0 max_bin_size: 943718400 max_ios_inflight: 1024 methylation-TAPS: false methylation-compress-cx-report: false methylation-generate-cytosine-report: false methylation-generate-mbias-report: false methylation-keep-ref-cytosine: false methylation-mapping-implementation: single-pass methylation-match-bismark: false methylation-protocol: none methylation-reports-only: false min-predicted-output-gb: 200 multiplier: 1 no-reset: false output-directory: RnaDragenCaller output-file-prefix: TVR0014-R03-P01-A00 output-format: bam pair-by-name: true pair-suffix-delimiter: / partition-on-compression-bottleneck: false pe-stats-continuous-update: false pe-stats-interval-delay: 5 pe-stats-interval-memory: 10 pe-stats-interval-size: 25000 pe-stats-sample-size: 100000 pe-stats-update-log-only: false preserve-bqsr-tags: false preserve-map-align-order: false qc-coverage-filters-1: countduplicate qc-coverage-ignore-overlaps: true qc-coverage-region-1: resource_bundle/dragen/MixRNA_Manifest.bed qc-coverage-region-2: resource_bundle/dragen/MixRNA_Manifest.bed qc-coverage-region-3: resource_bundle/qcresources/MixRNA_Manifest.exon.bed qc-coverage-reports-3: cov_report  qc-coverage-tag-1: duped qc-coverage-tag-2: deduped qc-coverage-tag-3: exon qc-indel-denovo-quality-threshold: 0.02 qc-snp-denovo-quality-threshold: 0.050000000000000003 read-trimmers: cut-end recordset-memory: 1073741824 ref-dir: hashtable ref-load-hash-bin: true reg_errors_are_warnings: 0 remove-duplicates: false repeat-genotype-enable: false repeat-genotype-min-anchor-mapq: 60 repeat-genotype-min-baseq: 20 repeat-genotype-min-score: 0.90000000000000002 repeat-genotype-read-depth: 0 repeat-genotype-read-length: 0 repeat-genotype-region-extension-length: 1000 repeat-genotype-skip-unaligned: true repeat-genotype-specs:  rna-ann-sj-min-len: 6 rna-cv-min-expression: 500 rna-gf-aggressive-filters: false rna-gf-allow-overlapping-genes: false rna-gf-avg-mapq-threshold-div: 5 rna-gf-blast-pairs: resource_bundle/dragen/hg19_unassigned_TSO500.cdsplus.fa.allvsall.outfmt6.genesym.gz rna-gf-coverage-lookup-window: 1000 rna-gf-enable-read-share-cleanup: true rna-gf-enriched-genes: resource_bundle/dragen/TST170_RNAgenes_v2.txt rna-gf-enriched-only: true rna-gf-enriched-regions:  rna-gf-exon-snap: 50 rna-gf-filter-chrm: true rna-gf-mate-overhang: 8 rna-gf-max-partners: 3 rna-gf-merge-calls: true rna-gf-min-alt-to-ref: 0.00999999978 rna-gf-min-anchor: 12 rna-gf-min-blast-pairs-eval: 1e-100 rna-gf-min-breakpoint-distance: 0 rna-gf-min-breakpoint-mapq: 20 rna-gf-min-cis-distance: 200000 rna-gf-min-covered-bases: 125 rna-gf-min-covered-bases-uncaptured: 79 rna-gf-min-neighbor-dist: 15 rna-gf-min-nonref-split-support: 4 rna-gf-min-score: 0.5 rna-gf-min-score-ratio: 0.150000006 rna-gf-min-support: 5 rna-gf-min-support-be: 10 rna-gf-min-unique-alignments: 5 rna-gf-num-threads: 4 rna-gf-ref-anchor: 8 rna-gf-report-antisense: true rna-gf-report-intergenic: false rna-gf-report-intronic: true rna-gf-restrict-genes: false rna-gf-score-model:  rna-gf-split-percent-align: 0.600000024 rna-library-type: A rna-mapq-unique: 0 rna-quantification-fld-max: 1000 rna-quantification-fld-mean: 250 rna-quantification-fld-sd: 25 rna-quantification-full-concordance: false rna-quantification-gc-bias: true rna-quantification-inference-max: 10000 rna-quantification-inference-min: 100 rna-quantification-init-uniform: 0 rna-quantification-tlen-min: 500 rna-quantification-use-em: 0 rna-repeat-genes:  rna-repeat-intervals: resource_bundle/dragen/rna_repeats_hg19.bed rna-sjs-max-size: 1000000000 rna_aligner_buffer_size: 67108864 rna_aligner_buffers: 0 rrna-filter-enable: false rrna-filter-mode: 3 rrna-filter-score-bonus-coeff: 0.025000000000000001 rrna-filter-score-bonus-const: 2 s2c_dbam_block_size: 65536 s2c_dbam_pool_size: 32 s2c_decomp_block_size: 262144 s2c_decomp_pool_size: 64 s2c_graph_block_size: 16384 s2c_graph_pool_size: 256 s2c_hmm_block_size: 16384 s2c_hmm_pool_size: 16384 s2c_phase1_packet_size: 16384 s2c_phase2_packet_size: 16384 s2c_smw_block_size: 16384 s2c_smw_pool_size: 2048 scrna-count-introns: false scrna-global-umi: false single-cell-number-cells: 3000 single-cell-number-threads: 48 single-cell-threshold: ratio soft-read-trimmers: polyg sort_buffer_size: 1048576 stop-at-read: 0 strip-input-qname-suffixes: true sv-denovo-threshold: 20 sv-enable-rrm-for-insertions-in-cancer-calling-modes: true sv-enable-rrm-for-insertions-in-germline-calling-modes: true sv-filtered-contigs: *_random chrUn_* *_alt HLA-* GL*  sv-min-diploid-variant-score: 10 sv-min-pass-diploid-gt-score: 5 sv-min-pass-diploid-variant-score: 20 sv-min-pass-somatic-score: 30 sv-min-somatic-score: 10 sv-report-small-dup-as-ins: true trim-disable-mapping: false trim-filter-dummy-len: 10 trim-filter-set-flag: true trim-max-length: 76 trim-min-len-read1: 20 trim-min-len-read2: 20 trim-min-length: 20 trim-polyg-early-exit-threshold: -500 trim-polyg-g-score-r1-3prime: 15 trim-polyg-g-score-r1-5prime: 0 trim-polyg-g-score-r2-3prime: 15 trim-polyg-g-score-r2-5prime: 0 trim-polyg-kmer-len: 25 trim-polyg-kmer-non-g: 2 trim-polyg-min-trim-r1-3prime: 6 trim-polyg-min-trim-r1-5prime: 6 trim-polyg-min-trim-r2-3prime: 6 trim-polyg-min-trim-r2-5prime: 6 tso500-solid-rna: true tso500-use-combined-license: true umi-base-representation-min-ratio: 0.5 umi-correction-scheme: lookup umi-emit-multiplicity: both umi-enable: false umi-enable-contextual-corrections: true umi-enable-probability-model-merging: false umi-enable-shift-corrections: true umi-enable-trimming: true umi-end-mask-length: 0 umi-generate-bam-tags: true umi-generate-error-rate-bam-tags: false umi-masked-base-qual: 1 umi-max-base-quality: 63 umi-max-collision-rate: 1000 umi-max-read-error-rate: 1 umi-mem-throttle-gb: 30 umi-min-consensus-base-quality: 0 umi-min-input-base-quality: 0 umi-min-map-quality: 0 umi-min-reads-per-region: 4096 umi-min-supporting-reads: 2 umi-padding: A umi-preserve-input-tags: false umi-probability-merging-duplex-merging-thres: 1 umi-probability-merging-max-transition-ratio: 100000000 umi-probability-merging-min-isize-freq: 0.001 umi-probability-merging-seq-error: 0.001 umi-probability-merging-simplex-fuzzy-merging-thres: 1 umi-probability-merging-simplex-merging-thres: 1 umi-r1-length: 0 umi-random-merge-factor: 2 umi-read-minority-min-ratio: 0.5 umi-soft-clip-ratio: 0.5 umi-source: qname umi-start-mask-length: 0 umi-stat-estimation-max-fragment-count: 10 umi-stat-estimation-max-fragment-size: 1000 umi-stat-estimation-max-interval-number: 10 umi-stat-estimation-min-probability-unique-fragment: 0.998 umi-stat-estimation-umi-jumping-estimation-method: simplex umi-trim-allowed-mismatches: 1 umi-verbose-metrics: false use-mock-config: false vc-active-only: false vc-decoy-contigs: NC_007605 hs37d5 chrUn_KN707*v1_decoy chrUn_JTFH0100*v1_decoy KN707*.1 JTFH0100*.1 chrEBV CMV HBV HCV* HIV* KSHV HTLV* MCV SV40 HPV*  vc-emit-ref-confidence: NONE vc-emit-zero-coverage-intervals: true vc-enable-basecall-filter: false vc-enable-deterministic-run: true vc-enable-hw-hmm: true vc-enable-hw-hmm-dump-receiver-data: false vc-enable-hw-hmm-dump-sender-data: false vc-enable-hw-hmm-dump-worker-data: false vc-enable-hw-smw: true vc-enable-hw-smw-dump-receiver-data: false vc-enable-hw-smw-dump-sender-data: false vc-enable-hw-smw-dump-worker-data: false vc-hw-hmm-timeout: 100000 vc-limit-genomecov-output: false vc-max-alternate-alleles: 6 vc-max-haps-per-job: 2 vc-sw-cell-width: 16 vc-sw-instruction-set: sse2 vc-sw-mode: 0 vd-output-match-log: false vqsr-lod-cutoff: -5.0 vqsr-num-gaussians: 8,2,4,2 watchdog-active-timeout: 600 watchdog-dump-processes: true; watchdog-exit-on-hang: true watchdog-freemem-threshold: 2GB watchdog-idle-timeout: 600 watchdog-max-threads: 8388608 watchdog-poll-interval: 1 watchdog-resources-monitored: THREADS IO MEMORY  watchdog-verbose-logging: true num-engines: 5  Aligner.HardClipTags: 1  Aligner.HardClips: 6  Aligner.aln-min-score: 22  Aligner.bed-base-div64: 24571868  Aligner.clip-pe-overhang: 0  Aligner.give-pair-score: 1  Aligner.idx-base-div64: 23827264  Aligner.intr-motif0-pen: 30  Aligner.intr-motif12-pen: 5  Aligner.intr-motif34-pen: 15  Aligner.intr-motif56-pen: 20  Aligner.mapq-coeff-scaled: 38912  Aligner.match-n-score: 31  Aligner.methyl-aln-mode: 0  Aligner.ref-base-div64: 0  Aligner.rrna-bonus-coeff: 0  Aligner.rrna-bonus-const: 0  Aligner.rrna-mode: 0  Aligner.rrna-ref-id: 0  Aligner.seed-len-inv: 195  Aligner.steer-delta: 12  Aligner.stitch-skip-bias: 25  Aligner.supp-min-score-adj: 0  Mapper.adapter-detect-0: 2284439564 0  Mapper.adapter-detect-1: 2809932556 0  Mapper.adapter-detect-10: 0 0  Mapper.adapter-detect-11: 0 0  Mapper.adapter-detect-12: 0 0  Mapper.adapter-detect-13: 0 0  Mapper.adapter-detect-14: 0 0  Mapper.adapter-detect-15: 0 0  Mapper.adapter-detect-2: 3533599244 0  Mapper.adapter-detect-3: 870182156 0  Mapper.adapter-detect-4: 0 0  Mapper.adapter-detect-5: 0 0  Mapper.adapter-detect-6: 0 0  Mapper.adapter-detect-7: 0 0  Mapper.adapter-detect-8: 0 0  Mapper.adapter-detect-9: 0 0  Mapper.adapter-min-trim: 4  Mapper.adapter-trim-r1-3p-s0-p0: 0  Mapper.adapter-trim-r1-3p-s0-p1: 0  Mapper.adapter-trim-r1-3p-s0-p2: 0  Mapper.adapter-trim-r1-3p-s0-p3: 0  Mapper.adapter-trim-r1-3p-s1-p0: 0  Mapper.adapter-trim-r1-3p-s1-p1: 0  Mapper.adapter-trim-r1-3p-s1-p2: 0  Mapper.adapter-trim-r1-3p-s1-p3: 0  Mapper.adapter-trim-r1-3p-s2-p0: 0  Mapper.adapter-trim-r1-3p-s2-p1: 0  Mapper.adapter-trim-r1-3p-s2-p2: 0  Mapper.adapter-trim-r1-3p-s2-p3: 0  Mapper.adapter-trim-r1-3p-s3-p0: 0  Mapper.adapter-trim-r1-3p-s3-p1: 0  Mapper.adapter-trim-r1-3p-s3-p2: 0  Mapper.adapter-trim-r1-3p-s3-p3: 0  Mapper.adapter-trim-r1-3p-s4-p0: 0  Mapper.adapter-trim-r1-3p-s4-p1: 0  Mapper.adapter-trim-r1-3p-s4-p2: 0  Mapper.adapter-trim-r1-3p-s4-p3: 0  Mapper.adapter-trim-r1-3p-s5-p0: 0  Mapper.adapter-trim-r1-3p-s5-p1: 0  Mapper.adapter-trim-r1-3p-s5-p2: 0  Mapper.adapter-trim-r1-3p-s5-p3: 0  Mapper.adapter-trim-r1-3p-s6-p0: 0  Mapper.adapter-trim-r1-3p-s6-p1: 0  Mapper.adapter-trim-r1-3p-s6-p2: 0  Mapper.adapter-trim-r1-3p-s6-p3: 0  Mapper.adapter-trim-r1-3p-s7-p0: 0  Mapper.adapter-trim-r1-3p-s7-p1: 0  Mapper.adapter-trim-r1-3p-s7-p2: 0  Mapper.adapter-trim-r1-3p-s7-p3: 0  Mapper.adapter-trim-r1-5p-s0-p0: 0  Mapper.adapter-trim-r1-5p-s0-p1: 0  Mapper.adapter-trim-r1-5p-s0-p2: 0  Mapper.adapter-trim-r1-5p-s0-p3: 0  Mapper.adapter-trim-r1-5p-s1-p0: 0  Mapper.adapter-trim-r1-5p-s1-p1: 0  Mapper.adapter-trim-r1-5p-s1-p2: 0  Mapper.adapter-trim-r1-5p-s1-p3: 0  Mapper.adapter-trim-r1-5p-s2-p0: 0  Mapper.adapter-trim-r1-5p-s2-p1: 0  Mapper.adapter-trim-r1-5p-s2-p2: 0  Mapper.adapter-trim-r1-5p-s2-p3: 0  Mapper.adapter-trim-r1-5p-s3-p0: 0  Mapper.adapter-trim-r1-5p-s3-p1: 0  Mapper.adapter-trim-r1-5p-s3-p2: 0  Mapper.adapter-trim-r1-5p-s3-p3: 0  Mapper.adapter-trim-r1-5p-s4-p0: 0  Mapper.adapter-trim-r1-5p-s4-p1: 0  Mapper.adapter-trim-r1-5p-s4-p2: 0  Mapper.adapter-trim-r1-5p-s4-p3: 0  Mapper.adapter-trim-r1-5p-s5-p0: 0  Mapper.adapter-trim-r1-5p-s5-p1: 0  Mapper.adapter-trim-r1-5p-s5-p2: 0  Mapper.adapter-trim-r1-5p-s5-p3: 0  Mapper.adapter-trim-r1-5p-s6-p0: 0  Mapper.adapter-trim-r1-5p-s6-p1: 0  Mapper.adapter-trim-r1-5p-s6-p2: 0  Mapper.adapter-trim-r1-5p-s6-p3: 0  Mapper.adapter-trim-r1-5p-s7-p0: 0  Mapper.adapter-trim-r1-5p-s7-p1: 0  Mapper.adapter-trim-r1-5p-s7-p2: 0  Mapper.adapter-trim-r1-5p-s7-p3: 0  Mapper.adapter-trim-r2-3p-s0-p0: 0  Mapper.adapter-trim-r2-3p-s0-p1: 0  Mapper.adapter-trim-r2-3p-s0-p2: 0  Mapper.adapter-trim-r2-3p-s0-p3: 0  Mapper.adapter-trim-r2-3p-s1-p0: 0  Mapper.adapter-trim-r2-3p-s1-p1: 0  Mapper.adapter-trim-r2-3p-s1-p2: 0  Mapper.adapter-trim-r2-3p-s1-p3: 0  Mapper.adapter-trim-r2-3p-s2-p0: 0  Mapper.adapter-trim-r2-3p-s2-p1: 0  Mapper.adapter-trim-r2-3p-s2-p2: 0  Mapper.adapter-trim-r2-3p-s2-p3: 0  Mapper.adapter-trim-r2-3p-s3-p0: 0  Mapper.adapter-trim-r2-3p-s3-p1: 0  Mapper.adapter-trim-r2-3p-s3-p2: 0  Mapper.adapter-trim-r2-3p-s3-p3: 0  Mapper.adapter-trim-r2-3p-s4-p0: 0  Mapper.adapter-trim-r2-3p-s4-p1: 0  Mapper.adapter-trim-r2-3p-s4-p2: 0  Mapper.adapter-trim-r2-3p-s4-p3: 0  Mapper.adapter-trim-r2-3p-s5-p0: 0  Mapper.adapter-trim-r2-3p-s5-p1: 0  Mapper.adapter-trim-r2-3p-s5-p2: 0  Mapper.adapter-trim-r2-3p-s5-p3: 0  Mapper.adapter-trim-r2-3p-s6-p0: 0  Mapper.adapter-trim-r2-3p-s6-p1: 0  Mapper.adapter-trim-r2-3p-s6-p2: 0  Mapper.adapter-trim-r2-3p-s6-p3: 0  Mapper.adapter-trim-r2-3p-s7-p0: 0  Mapper.adapter-trim-r2-3p-s7-p1: 0  Mapper.adapter-trim-r2-3p-s7-p2: 0  Mapper.adapter-trim-r2-3p-s7-p3: 0  Mapper.adapter-trim-r2-5p-s0-p0: 0  Mapper.adapter-trim-r2-5p-s0-p1: 0  Mapper.adapter-trim-r2-5p-s0-p2: 0  Mapper.adapter-trim-r2-5p-s0-p3: 0  Mapper.adapter-trim-r2-5p-s1-p0: 0  Mapper.adapter-trim-r2-5p-s1-p1: 0  Mapper.adapter-trim-r2-5p-s1-p2: 0  Mapper.adapter-trim-r2-5p-s1-p3: 0  Mapper.adapter-trim-r2-5p-s2-p0: 0  Mapper.adapter-trim-r2-5p-s2-p1: 0  Mapper.adapter-trim-r2-5p-s2-p2: 0  Mapper.adapter-trim-r2-5p-s2-p3: 0  Mapper.adapter-trim-r2-5p-s3-p0: 0  Mapper.adapter-trim-r2-5p-s3-p1: 0  Mapper.adapter-trim-r2-5p-s3-p2: 0  Mapper.adapter-trim-r2-5p-s3-p3: 0  Mapper.adapter-trim-r2-5p-s4-p0: 0  Mapper.adapter-trim-r2-5p-s4-p1: 0  Mapper.adapter-trim-r2-5p-s4-p2: 0  Mapper.adapter-trim-r2-5p-s4-p3: 0  Mapper.adapter-trim-r2-5p-s5-p0: 0  Mapper.adapter-trim-r2-5p-s5-p1: 0  Mapper.adapter-trim-r2-5p-s5-p2: 0  Mapper.adapter-trim-r2-5p-s5-p3: 0  Mapper.adapter-trim-r2-5p-s6-p0: 0  Mapper.adapter-trim-r2-5p-s6-p1: 0  Mapper.adapter-trim-r2-5p-s6-p2: 0  Mapper.adapter-trim-r2-5p-s6-p3: 0  Mapper.adapter-trim-r2-5p-s7-p0: 0  Mapper.adapter-trim-r2-5p-s7-p1: 0  Mapper.adapter-trim-r2-5p-s7-p2: 0  Mapper.adapter-trim-r2-5p-s7-p3: 0  Mapper.alt-aware: 0  Mapper.chain-filt-ratio: 1024  Mapper.pri-crc-poly: 2C991CE6A8DD55  Mapper.sec-crc-poly: 1524CA66E8D39  Mapper.cut-bases: 0  Mapper.edit-pattern: 1  Mapper.edit-period: 15  Mapper.edit-seeds-limit: 6  Mapper.enable-anchors: 0  Mapper.enable-ann-sjs: 1  Mapper.extab-base-div64: 477649776  Mapper.filter-dummy-len: 10  Mapper.max-read-len: 4980812  Mapper.methyl-map-mode: 0  Mapper.min-read-len: 1310740  Mapper.min-trim-bases: 0  Mapper.polyg-early-exit: 4294966796  Mapper.polyg-g-score: 251662080  Mapper.polyg-kmer-len: 25  Mapper.polyg-kmer-non-g: 2  Mapper.polyg-min-trim: 101058054  Mapper.pos-bin-gran-sel: 7  Mapper.pri-crc-bits: 54  Mapper.pri-seed-bases: 21  Mapper.qual-cutoff: 4294967295  Mapper.ref-alt-seed: 3049725952  Mapper.ref-seed-interval: 16  Mapper.rna-mode: 1  Mapper.sec-crc-bits: 49  Mapper.seed-pattern: 1  Mapper.seed-period: 2  Mapper.sjs-base-div64: 529878124  Mapper.table-base-div64: 24664944  Mapper.table-size-64ths: 54  Mapper.trim-flags: 256  Mapper.trim-steps: 4294967063  Mapper.trim-steps-soft: 2 

Local App 2.2.0.12:

• Multiple files per sample
  • [file path for DNA samples, an intermediate alignment file: Logs_Intermediates/DnaAlignment/<sample_ID>/<sample_ID>.bam ]
  • [file path for DNA samples, an intermediate alignment file: Logs_Intermediates/DnaRealignment/<sample_ID>/<sample_ID>.bam ]
  • file path for DNA samples, the final alignment file: Logs_Intermediates/StitchedRealigned/<sample_ID>/<sample_ID>.bam
    • Corresponds to the Dragen BAM file

@HD	VN:1.5	SO:coordinate
@SQ	SN:chrM	LN:16571
@SQ	SN:chr1	LN:249250621
@SQ	SN:chr2	LN:243199373
@SQ	SN:chr3	LN:198022430
@SQ	SN:chr4	LN:191154276
@SQ	SN:chr5	LN:180915260
@SQ	SN:chr6	LN:171115067
@SQ	SN:chr7	LN:159138663
@SQ	SN:chr8	LN:146364022
@SQ	SN:chr9	LN:141213431
@SQ	SN:chr10	LN:135534747
@SQ	SN:chr11	LN:135006516
@SQ	SN:chr12	LN:133851895
@SQ	SN:chr13	LN:115169878
@SQ	SN:chr14	LN:107349540
@SQ	SN:chr15	LN:102531392
@SQ	SN:chr16	LN:90354753
@SQ	SN:chr17	LN:81195210
@SQ	SN:chr18	LN:78077248
@SQ	SN:chr19	LN:59128983
@SQ	SN:chr20	LN:63025520
@SQ	SN:chr21	LN:48129895
@SQ	SN:chr22	LN:51304566
@SQ	SN:chrX	LN:155270560
@SQ	SN:chrY	LN:59373566
@PG	ID:bwa	PN:bwa	VN:0.7.17-r1188	CL:/opt/illumina/components/bwa mem -t 26 -K 160000000 -C /opt/illumina/resources/genomes/hg19_hardPAR/genome.fa /opt/illumina/analysis-folder/cromwell-executions/TSO500/e6fb2bce-1faa-45b3-b348-e0c4df2df67a/call-DnaSubWorkflow/DnaSubWorkflow/03029381-66b0-4837-8b3a-0cb39afaeca7/call-DnaRealignmentTask/tmp.12082042/pipe.r1.AG44 /opt/illumina/analysis-folder/cromwell-executions/TSO500/e6fb2bce-1faa-45b3-b348-e0c4df2df67a/call-DnaSubWorkflow/DnaSubWorkflow/03029381-66b0-4837-8b3a-0cb39afaeca7/call-DnaRealignmentTask/tmp.12082042/pipe.r2.2v9e
@PG	ID:reco	PN:reco	VN:x.x.x.x
@PG	ID:samtools	PN:samtools	PP:bwa	VN:1.7	CL:/opt/illumina/components/samtools reheader - /opt/illumina/analysis-folder/Logs_Intermediates/DnaRealignment/TVD0016-D01-P01-A00/TVD0016-D01-P01-A00.bam.tmp
@PG	ID:samtools.1	PN:samtools	PP:reco	VN:1.7	CL:/opt/illumina/components/samtools reheader - /opt/illumina/analysis-folder/Logs_Intermediates/DnaRealignment/TVD0016-D01-P01-A00/TVD0016-D01-P01-A00.bam.tmp
@PG	ID:Gemini PN:Gemini VN:5.2.11.69 CL:/opt/illumina/components/Gemini/Gemini.dll-bam/opt/illumina/analysis-folder/Logs_Intermediates/DnaRealignment/TVD0016-D01-P01-A00/TVD0016-D01-P01-A00.bam-genome/opt/illumina/resources/genomes/hg19_hardPAR-samtools/opt/illumina/components/samtools--trustsoftclipsfalse--remaskmessysoftclipstrue--nifydisagreementtrue--ignorereadsabovemaxlengthtrue--dontstitchrepeatoverlaptrue--filterforproperpairstrue--treatabnormalorientationasimpropertrue--checksoftclipsformismatchestrue--trackmismatchestrue--softclipunknownindelstrue--categoriestorealignImperfectStitched,FailStitch,UnstitchIndel,Unstitchable,Disagree,MessyStitched,MessySplit,UnstitchImperfect,LongFragment,UnstitchMessy,UnstitchForwardMessy,UnstitchReverseMessy,IndelSingleton,IndelUnstitchable,UnstitchMessyIndel,UnstitchMessySuspiciousRead,UnstitchMessyIndelSuspiciousRead,UnstitchReverseMessyIndel,UnstitchForwardMessyIndel,UnstitchMessySuspiciousMd--categoriestosnowballUnstitchIndel,MessyStitched,UnstitchMessy,MessySplit--minpreferredsupport1--minpreferredanchor7--binsize1--messysitewidth500--imperfectfreqthreshold0.01--indelregionfreqthreshold0.001--regionsize1000000--messymapq50--directionalmessthreshold0.1--silencedirectionalmessreadstrue--silencemessymapmessreadstrue--silencesuspiciousmdreadstrue--chromRefId0--outFolder/opt/illumina/analysis-folder/Logs_Intermediates/StitchedRealigned/8648dea9-f42f-41f8-a967-d60ddc0ba6bb/TVD0016-D01-P01-A00/chrM

• [file path for RNA samples, an intermediate alignment file: Logs_Intermediates/RnaAlignment/<sample_ID>/<sample_ID>.bam ]
• file path for RNA samples, the final alignment file: Logs_Intermediates/RnaMarkDuplicates/<sample_ID>/<sample_ID>.bam
  • Corresponds to the Dragen BAM file

@HD	VN:1.4	SO:coordinate
@SQ	SN:chrM	LN:16571
@SQ	SN:chr1	LN:249250621
@SQ	SN:chr2	LN:243199373
@SQ	SN:chr3	LN:198022430
@SQ	SN:chr4	LN:191154276
@SQ	SN:chr5	LN:180915260
@SQ	SN:chr6	LN:171115067
@SQ	SN:chr7	LN:159138663
@SQ	SN:chr8	LN:146364022
@SQ	SN:chr9	LN:141213431
@SQ	SN:chr10	LN:135534747
@SQ	SN:chr11	LN:135006516
@SQ	SN:chr12	LN:133851895
@SQ	SN:chr13	LN:115169878
@SQ	SN:chr14	LN:107349540
@SQ	SN:chr15	LN:102531392
@SQ	SN:chr16	LN:90354753
@SQ	SN:chr17	LN:81195210
@SQ	SN:chr18	LN:78077248
@SQ	SN:chr19	LN:59128983
@SQ	SN:chr20	LN:63025520
@SQ	SN:chr21	LN:48129895
@SQ	SN:chr22	LN:51304566
@SQ	SN:chrX	LN:155270560
@SQ	SN:chrY	LN:59373566
@SQ	SN:chrUn_gl000211	LN:166566
@SQ	SN:chrUn_gl000212	LN:186858
@SQ	SN:chrUn_gl000213	LN:164239
@SQ	SN:chrUn_gl000214	LN:137718
@SQ	SN:chrUn_gl000215	LN:172545
@SQ	SN:chrUn_gl000216	LN:172294
@SQ	SN:chrUn_gl000217	LN:172149
@SQ	SN:chrUn_gl000218	LN:161147
@SQ	SN:chrUn_gl000219	LN:179198
@SQ	SN:chrUn_gl000220	LN:161802
@SQ	SN:chrUn_gl000221	LN:155397
@SQ	SN:chrUn_gl000222	LN:186861
@SQ	SN:chrUn_gl000223	LN:180455
@SQ	SN:chrUn_gl000224	LN:179693
@SQ	SN:chrUn_gl000225	LN:211173
@SQ	SN:chrUn_gl000226	LN:15008
@SQ	SN:chrUn_gl000227	LN:128374
@SQ	SN:chrUn_gl000228	LN:129120
@SQ	SN:chrUn_gl000229	LN:19913
@SQ	SN:chrUn_gl000230	LN:43691
@SQ	SN:chrUn_gl000231	LN:27386
@SQ	SN:chrUn_gl000232	LN:40652
@SQ	SN:chrUn_gl000233	LN:45941
@SQ	SN:chrUn_gl000234	LN:40531
@SQ	SN:chrUn_gl000235	LN:34474
@SQ	SN:chrUn_gl000236	LN:41934
@SQ	SN:chrUn_gl000237	LN:45867
@SQ	SN:chrUn_gl000238	LN:39939
@SQ	SN:chrUn_gl000239	LN:33824
@SQ	SN:chrUn_gl000240	LN:41933
@SQ	SN:chrUn_gl000241	LN:42152
@SQ	SN:chrUn_gl000242	LN:43523
@SQ	SN:chrUn_gl000243	LN:43341
@SQ	SN:chrUn_gl000244	LN:39929
@SQ	SN:chrUn_gl000245	LN:36651
@SQ	SN:chrUn_gl000246	LN:38154
@SQ	SN:chrUn_gl000247	LN:36422
@SQ	SN:chrUn_gl000248	LN:39786
@SQ	SN:chrUn_gl000249	LN:38502
@PG	ID:STAR	PN:STAR	VN:STAR_2.6.1c	CL:/opt/illumina/components/STAR/STAR   --runThreadN 32   --genomeDir /opt/illumina/resources/star/hg19_unassigned_STARindex/STARindex   --genomeLoad LoadAndKeep   --readFilesIn /opt/illumina/analysis-folder/Logs_Intermediates/TrimFastq/TVR0014-R03-P01-A00/TVR0014-R03-P01-A00_S14_L001_R1_001.fastq.gz,/opt/illumina/analysis-folder/Logs_Intermediates/TrimFastq/TVR0014-R03-P01-A00/TVR0014-R03-P01-A00_S14_L002_R1_001.fastq.gz,/opt/illumina/analysis-folder/Logs_Intermediates/TrimFastq/TVR0014-R03-P01-A00/TVR0014-R03-P01-A00_S14_L003_R1_001.fastq.gz,/opt/illumina/analysis-folder/Logs_Intermediates/TrimFastq/TVR0014-R03-P01-A00/TVR0014-R03-P01-A00_S14_L004_R1_001.fastq.gz   /opt/illumina/analysis-folder/Logs_Intermediates/TrimFastq/TVR0014-R03-P01-A00/TVR0014-R03-P01-A00_S14_L001_R2_001.fastq.gz,/opt/illumina/analysis-folder/Logs_Intermediates/TrimFastq/TVR0014-R03-P01-A00/TVR0014-R03-P01-A00_S14_L002_R2_001.fastq.gz,/opt/illumina/analysis-folder/Logs_Intermediates/TrimFastq/TVR0014-R03-P01-A00/TVR0014-R03-P01-A00_S14_L003_R2_001.fastq.gz,/opt/illumina/analysis-folder/Logs_Intermediates/TrimFastq/TVR0014-R03-P01-A00/TVR0014-R03-P01-A00_S14_L004_R2_001.fastq.gz      --readFilesCommand zcat      --limitBAMsortRAM 12000000000   --outFileNamePrefix /opt/illumina/analysis-folder/Logs_Intermediates/RnaAlignment/TVR0014-R03-P01-A00/TVR0014-R03-P01-A00-   --outSAMtype BAM   SortedByCoordinate      --outSAMstrandField intronMotif   --outSAMattributes NH   NM   MD      --outSAMunmapped Within      --outSAMmapqUnique 50   --outSAMattrRGline "ID:001 SM:TVR0014-R03-P01-A00"      --outSAMtlen 2   --outSJfilterCountUniqueMin -1   2   2   2      --outSJfilterCountTotalMin -1   2   2   2      --outFilterType BySJout   --outFilterIntronMotifs RemoveNoncanonical   --peOverlapNbasesMin 10   --peOverlapMMp 0.1   --chimSegmentMin 12   --chimScoreDropMax 20   --chimScoreSeparation 5   --chimScoreJunctionNonGTAG -100   --chimJunctionOverhangMin 12   --chimOutType WithinBAM      --chimSegmentReadGapMax 5
@PG	ID:samtools	PN:samtools	PP:STAR	VN:1.11	CL:/data/programs/samtools-1.11/samtools view -H ./Logs_Intermediates/RnaMarkDuplicates/TVR0014-R03-P01-A00/TVR0014-R03-P01-A00.bam
@RG	ID:001 SM:TVR0014-R03-P01-A00
@CO	user command line: /opt/illumina/components/STAR/STAR --genomeDir /opt/illumina/resources/star/hg19_unassigned_STARindex/STARindex --readFilesIn /opt/illumina/analysis-folder/Logs_Intermediates/TrimFastq/TVR0014-R03-P01-A00/TVR0014-R03-P01-A00_S14_L001_R1_001.fastq.gz,/opt/illumina/analysis-folder/Logs_Intermediates/TrimFastq/TVR0014-R03-P01-A00/TVR0014-R03-P01-A00_S14_L002_R1_001.fastq.gz,/opt/illumina/analysis-folder/Logs_Intermediates/TrimFastq/TVR0014-R03-P01-A00/TVR0014-R03-P01-A00_S14_L003_R1_001.fastq.gz,/opt/illumina/analysis-folder/Logs_Intermediates/TrimFastq/TVR0014-R03-P01-A00/TVR0014-R03-P01-A00_S14_L004_R1_001.fastq.gz /opt/illumina/analysis-folder/Logs_Intermediates/TrimFastq/TVR0014-R03-P01-A00/TVR0014-R03-P01-A00_S14_L001_R2_001.fastq.gz,/opt/illumina/analysis-folder/Logs_Intermediates/TrimFastq/TVR0014-R03-P01-A00/TVR0014-R03-P01-A00_S14_L002_R2_001.fastq.gz,/opt/illumina/analysis-folder/Logs_Intermediates/TrimFastq/TVR0014-R03-P01-A00/TVR0014-R03-P01-A00_S14_L003_R2_001.fastq.gz,/opt/illumina/analysis-folder/Logs_Intermediates/TrimFastq/TVR0014-R03-P01-A00/TVR0014-R03-P01-A00_S14_L004_R2_001.fastq.gz --outSAMattrRGline "ID:001 SM:TVR0014-R03-P01-A00" --genomeLoad LoadAndKeep --runThreadN 32 --outFileNamePrefix /opt/illumina/analysis-folder/Logs_Intermediates/RnaAlignment/TVR0014-R03-P01-A00/TVR0014-R03-P01-A00- --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMattributes NH NM MD --outSAMmapqUnique 50 --outSAMstrandField intronMotif --outFilterType BySJout --outSJfilterCountUniqueMin -1 2 2 2 --outSJfilterCountTotalMin -1 2 2 2 --outFilterIntronMotifs RemoveNoncanonical --chimScoreSeparation 5 --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimScoreDropMax 20 --chimSegmentReadGapMax 5 --chimOutType WithinBAM --limitBAMsortRAM 12000000000 --peOverlapNbasesMin 10 --peOverlapMMp 0.1 --outSAMtlen 2 --chimScoreJunctionNonGTAG -100

4.2. Notable differences between Dragen and Local App output files

• Difference in the contig list (see header lines tagged with @SQ), mainly in the DNA alignments
  • Any implications for misalignments?
• Noticeable differences in coverages/read counts (as visible in IGV and as reported in the sample metrics)
  • This impacts many metrics
• Read groups (see the @RG tags in the headers above) are missing in DNA alignments generated by the Local App, but not in Dragen's output
  • Read groups are necessary for running GATK tools (when using Dragen-generated BAM files, one doesn't need to add read groups prior to running GATK on the data)

4.3. Alignment data usage in tsoppy modules

4.3.1. Modules that would utilize the alignment data

• Allele-specific copy number analysis tools (PureCN and CANCAN)
• RNA/DNA coverage profile plotting (e.g., coverage shifts at fusion break-points, coverage drops/gains at deletions/internal tandem repeat hotspots) [not currently offered by TSOPPI, but used experimentally at OUS]
• Checking of RNA-support for variants detected in DNA

4.3.2. Suggestions for implementation

• As a standard format, both Dragen and Local App files should be directly usable in most analyses
  • Missing read group information in the Local App-generated DNA sample BAM files does imply an extra pre-processing step compared to Dragen output processing (whenever GATK tools become involved)
• The reasons behind- and implications of- 1) different contig lists and 2) absolute coverage differences should be further explored before Local App and Dragen BAM files are used interchangeably in post-processing

[marrip]

• Logs_Intermediates/DnaRealignment/*/*.bam -> 05_PCGR_to_IGV_links.py
• Logs_Intermediates/StitchedRealigned/*/*.bam -> PureCN/Coverage.R; PureCN/PureCN.R; 05_PCGR_to_IGV_links.py
• Logs_Intermediates/RnaMarkDuplicates/*/*.bam -> 05_PCGR_to_IGV_links.py; 02_TSO_500_small_variant_aggregation.py

Should we add the RG automatically if the input is from LocalApp? This would be part of the nextflow pipeline which can check and run the task if necessary. What do you think?

[danielvo]

I expect the samtools and picard tools to be equivalent when it comes to the 'adding read groups' functionality (I am just personally used to running picard tools for this task). I also suspect that we might end up using both tools (samtools and picard) in other contexts, so I have no clear preference in this particular example.

[marrip]

If there is no difference in the output, I think we can decide on what you guys agree on. Do you think that you need to use samtools to be compatible with the pysam library, @tinavisnovska ?

[tinavisnovska]

pysam provides python api to samtools functionality so adding read groups that way would be a bit more elegant that way,... however, I am not sure pysam is the best option for vcfs due to binary representation of floating points and rounding issues that can occur for any threashold we would try to use,...

[marrip]

if we can use a open source tool for doing something like adding read groups I would default to the tool unless it gives us any advantage of doing that in tsoppy directly.

[marrip]

if pysam is not feasible for us then we can disregard it and do samtools/Picard as before.