/
rd_dna_parameters.yaml
executable file
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/
rd_dna_parameters.yaml
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---
## Version: 2.1.0
custom_default_parameters:
associated_recipe:
- mip
data_type: ARRAY
default:
- analysis_type
- conda_path
- bwa_build_reference
- bwa_mem2_build_reference
- exome_target_bed
- infile_dirs
- install_config_file
- pedigree_fam_file
- picardtools_path
- reference_dir
- reference_info_file
- rtg_vcfeval_reference_genome
- sample_info_file
- store_file
- sv_vcfparser_select_file
- temp_directory
- vcfparser_select_file
type: mip
decompose_normalize_references:
associated_recipe:
- mip
data_type: ARRAY
default:
- gatk_baserecalibration_known_sites
- gatk_haplotypecaller_snp_known_set
- gatk_varianteval_dbsnp
- gatk_varianteval_gold
- gatk_variantrecalibration_resource_indel
- sv_vcfanno_config
- vcfanno_config
type: mip
exome_target_bed:
associated_recipe:
- picardtools_collecthsmetrics
- gatk_baserecalibration
- gatk_haplotypecaller
build_file: 1
data_type: HASH
exists_check: file
is_reference: 1
reference: reference_dir
type: path
expected_coverage:
associated_recipe:
- mip
data_type: HASH
mandatory: no
type: mip
## genomeAnalysisToolKitPath
gatk_logging_level:
associated_recipe:
- gatk_baserecalibration
- gatk_combinevariantcallsets
- gatk_gathervcfs
- gatk_genotypegvcfs
- gatk_haplotypecaller
- gatk_variantevalall
- gatk_variantevalexome
- gatk_variantrecalibration
- rankvariant
- varianteffectpredictor
data_type: SCALAR
default: INFO
type: recipe_argument
gatk_path:
associated_recipe:
- gatk_combinevariantcallsets
- gatk_variantevalall
- gatk_variantevalexome
data_type: SCALAR
default: /usr/
type: path
## HumanGenomeReference
human_genome_reference:
associated_recipe:
- bwa_mem
- bwa_mem2
- cnvnator_ar
- delly_call
- expansionhunter
- gatk_baserecalibration
- gatk_haplotypecaller
- gatk_genotypegvcfs
- gatk_variantevalall
- gatk_variantevalexome
- gatk_variantrecalibration
- manta
- mip
- picardtools_collecthsmetrics
- picardtools_collectmultiplemetrics
- tiddit
- vt_ar
data_type: SCALAR
default: grch37_homo_sapiens_-d5-.fasta
exists_check: file
is_reference: 1
reference: reference_dir
type: path
human_genome_reference_file_endings:
associated_recipe:
- bwa_mem
- bwa_mem2
- cnvnator_ar
- delly_call
- expansionhunter
- gatk_baserecalibration
- gatk_haplotypecaller
- gatk_genotypegvcfs
- gatk_variantevalall
- gatk_variantevalexome
- gatk_variantrecalibration
- manta
- picardtools_collecthsmetrics
- picardtools_collectmultiplemetrics
- tiddit
- vt_ar
build_file: 1
data_type: SCALAR
exists_check: file
mandatory: no
reference: reference_dir
type: path
#### Bash
recipe_core_number:
associated_recipe:
- mip
data_type: HASH
default:
analysisrunstatus: 1
bwa_mem: 36
bwa_mem2: 36
cadd_ar: 13
chanjo_sexcheck: 1
chromograph_cov: 1
chromograph_upd: 1
cnvnator_ar: 13
deepvariant: 36
delly_call: 36
delly_reformat: 13
endvariantannotationblock: 1
expansionhunter: 0
fastqc_ar: 0
variant_annotation: 13
frequency_filter: 13
gatk_baserecalibration: 13
gatk_combinevariantcallsets: 1
gatk_gathervcfs: 1
gatk_genotypegvcfs: 1
gatk_haplotypecaller: 16
gatk_variantevalall: 1
gatk_variantevalexome: 1
gatk_variantrecalibration: 1
glnexus_merge: 1
gzip_fastq: 0
manta: 36
markduplicates: 13
multiqc_ar: 1
peddy_ar: 4
picardtools_collecthsmetrics: 1
picardtools_collectmultiplemetrics: 1
plink: 1
qccollect_ar: 1
rhocall_ar: 13
rhocall_viz: 1
rtg_vcfeval: 36
sacct: 1
sambamba_depth: 1
samtools_merge: 13
samtools_subsample_mt: 1
smncopynumbercaller: 4
star_caller: 4
split_fastq_file: 4
sv_annotate: 1
sv_combinevariantcallsets: 1
sv_rankvariant: 16
sv_reformat: 1
sv_varianteffectpredictor: 0
sv_vcfparser: 13
telomerecat_ar: 12
tiddit_coverage: 1
upd_ar: 1
varg_ar: 1
version_collect_ar: 1
vcf2cytosure_ar: 0
vt_ar: 13
vt_core: 1
type: mip
set_recipe_core_number:
associated_recipe:
- mip
data_type: HASH
mandatory: no
type: mip
## Memory per parallel process/core
recipe_memory:
associated_recipe:
- mip
data_type: HASH
default:
cadd_ar: 6
chanjo_sexcheck: 2
chromograph_cov: 5
chromograph_upd: 5
delly_reformat: 3
endvariantannotationblock: 8
expansionhunter: 2
variant_annotation: 3
gatk_baserecalibration: 10
gatk_combinevariantcallsets: 25
gatk_gathervcfs: 7
gatk_genotypegvcfs: 12
gatk_variantrecalibration: 30
glnexus_merge: 150
markduplicates: 10
picardtools_collecthsmetrics: 8
picardtools_collectmultiplemetrics: 8
plink: 10
rhocall_ar: 2
rhocall_viz: 5
sambamba_depth: 10
samtools_subsample_mt: 4
split_fastq_file: 2
sv_annotate: 7
sv_reformat: 24
sv_varianteffectpredictor: 9
tiddit: 8
upd_ar: 3
vcf2cytosure_ar: 6
varianteffectpredictor: 7
type: mip
set_recipe_memory:
associated_recipe:
- mip
data_type: HASH
mandatory: no
type: mip
recipe_time:
associated_recipe:
- mip
data_type: HASH
default:
analysisrunstatus: 1
bwa_mem: 30
bwa_mem2: 10
cadd_ar: 10
chanjo_sexcheck: 2
chromograph_cov: 1
chromograph_upd: 1
cnvnator_ar: 1
deepvariant: 10
delly_call: 20
delly_reformat: 7
endvariantannotationblock: 2
expansionhunter: 2
fastqc_ar: 10
variant_annotation: 3
frequency_filter: 2
gatk_baserecalibration: 20
gatk_combinevariantcallsets: 2
gatk_genotypegvcfs: 10
gatk_gathervcfs: 2
gatk_haplotypecaller: 30
gatk_variantevalall: 2
gatk_variantevalexome: 2
gatk_variantrecalibration: 10
glnexus_merge: 5
gzip_fastq: 2
manta: 30
markduplicates: 20
multiqc_ar: 5
peddy_ar: 1
picardtools_collecthsmetrics: 10
picardtools_collectmultiplemetrics: 10
plink: 1
prepareforvariantannotationblock: 5
qccollect_ar: 1
rankvariant: 10
rhocall_ar: 5
rhocall_viz: 1
rtg_vcfeval: 1
sacct: 1
sambamba_depth: 10
samtools_merge: 10
samtools_subsample_mt: 1
smncopynumbercaller: 1
split_fastq_file: 10
star_caller: 1
sv_annotate: 2
sv_combinevariantcallsets: 2
sv_rankvariant: 10
sv_reformat: 1
sv_varianteffectpredictor: 10
sv_vcfparser: 2
telomerecat_ar: 5
tiddit: 20
tiddit_coverage: 5
upd_ar: 1
varg_ar: 1
varianteffectpredictor: 10
vcf2cytosure_ar: 20
vcfparser_ar: 5
version_collect_ar: 1
vt_ar: 10
vt_core: 10
type: mip
set_recipe_time:
associated_recipe:
- mip
data_type: HASH
mandatory: no
type: mip
infile_dirs:
associated_recipe:
- mip
exists_check: directory
data_type: HASH
type: path
update_path: absolute_path
picardtools_path:
associated_recipe:
- bwa_mem
- bwa_mem2
- delly_reformat
- markduplicates
- picardtools_collecthsmetrics
- picardtools_collectmultiplemetrics
- sv_reformat
data_type: SCALAR
type: path
### Programs
split_fastq_file:
analysis_mode: sample
associated_recipe:
- mip
data_type: SCALAR
default: 0
file_tag: nofile_tag
outfile_suffix: ".fastq.gz"
program_executables:
- pigz
- split
type: recipe
split_fastq_file_read_batch:
associated_recipe:
- split_fastq_file
data_type: SCALAR
default: 25000000
type: recipe_argument
## Gzip
gzip_fastq:
analysis_mode: sample
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: nofile_tag
infile_suffix: ".fastq"
type: recipe
## FastQC
fastqc_ar:
analysis_mode: sample
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: nofile_tag
infile_suffix: ".fastq"
program_executables:
- fastqc
type: recipe
## BWA
bwa_mem:
analysis_mode: sample
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: _sorted
outfile_suffix: ".bam"
program_executables:
- bwa
- samtools
recipe_type: aligners
type: recipe
bwa_build_reference:
associated_recipe:
- bwa_mem
build_file: 1
data_type: SCALAR
exists_check: file
reference: reference_dir
type: path
bwa_mem2:
analysis_mode: sample
associated_recipe:
- mip
data_type: SCALAR
default: 0
file_tag: _sorted
outfile_suffix: ".bam"
program_executables:
- bwa-mem2
- samtools
recipe_type: aligners
type: recipe
bwa_mem2_build_reference:
associated_recipe:
- bwa_mem2
build_file: 1
data_type: SCALAR
exists_check: file
reference: reference_dir
type: path
bwa_mem_bamstats:
associated_recipe:
- bwa_mem
- bwa_mem2
data_type: SCALAR
default: 1
type: recipe_argument
bwa_mem_cram:
associated_recipe:
- bwa_mem
- bwa_mem2
data_type: SCALAR
default: 0
type: recipe_argument
bwa_mem_hla:
associated_recipe:
- bwa_mem
data_type: SCALAR
default: 0
type: recipe_argument
bwa_soft_clip_sup_align:
associated_recipe:
- bwa_mem
- bwa_mem2
data_type: SCALAR
default: 0
type: recipe_argument
samtools_merge:
analysis_mode: sample
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: ""
program_executables:
- samtools
outfile_suffix: ".bam"
type: recipe
markduplicates:
analysis_mode: sample
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: _md
outfile_suffix: ".bam"
program_executables:
- picard
type: recipe
markduplicates_picardtools_opt_dup_dist:
associated_recipe:
- markduplicates
data_type: SCALAR
default: 2500
type: recipe_argument
## Deepvariant
deepvariant:
analysis_mode: sample
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: _deepvar
outfile_suffix: ".g.vcf.gz"
program_executables:
- run_deepvariant
type: recipe
glnexus_merge:
analysis_mode: case
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: _glnex
outfile_suffix: ".vcf.gz"
program_executables:
- glnexus_cli
- bcftools
- bgzip
recipe_type: variant_callers
type: recipe
variant_caller: deepvariant
## GATK BAM Calibration
gatk_baserecalibration:
analysis_mode: sample
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: _brecal
outfile_suffix: ".bam"
program_executables:
- gatk
- samtools
type: recipe
gatk_baserecalibration_known_sites:
associated_recipe:
- gatk_baserecalibration
data_type: ARRAY
default:
- grch37_dbsnp_-138-.vcf
- grch37_1000g_indels_-phase1-.vcf
- grch37_mills_and_1000g_-gold_standard_indels-.vcf
exists_check: file
is_reference: 1
reference: reference_dir
type: path
gatk_baserecalibration_read_filters:
associated_recipe:
- gatk_baserecalibration
data_type: ARRAY
default:
- OverclippedReadFilter
type: recipe_argument
gatk_baserecalibration_static_quantized_quals:
associated_recipe:
- gatk_baserecalibration
data_type: ARRAY
mandatory: no
default:
- 10
- 20
- 30
- 40
type: recipe_argument
## Coverage Analysis
chanjo_sexcheck:
analysis_mode: sample
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: _sex
outfile_suffix: ".tsv"
program_executables:
- chanjo
type: recipe
chanjo_sexcheck_log_level:
associated_recipe:
- chanjo_sexcheck
data_type: SCALAR
default: DEBUG
type: recipe_argument
samtools_subsample_mt:
analysis_mode: sample
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: _subsample_MT
outfile_suffix: ".bam"
program_executables:
- samtools
type: recipe
samtools_subsample_mt_depth:
analysis_mode: sample
associated_recipe:
- samtools_subsample_mt
data_type: SCALAR
default: 150
type: recipe_argument
sambamba_depth:
analysis_mode: sample
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: _coverage
outfile_suffix: ".bed"
program_executables:
- sambamba
type: recipe
sambamba_depth_base_quality:
associated_recipe:
- sambamba_depth
data_type: SCALAR
default: 10
type: recipe_argument
sambamba_depth_bed:
associated_recipe:
- sambamba_depth
data_type: SCALAR
exists_check: file
reference: reference_dir
type: path
sambamba_depth_cutoffs:
associated_recipe:
- sambamba_depth
data_type: ARRAY
default:
- 10
- 15
- 20
- 50
- 100
type: recipe_argument
sambamba_depth_mode:
associated_recipe:
- sambamba_depth
data_type: SCALAR
default: region
type: recipe_argument
sambamba_depth_noduplicates:
associated_recipe:
- sambamba_depth
data_type: SCALAR
default: 1
type: recipe_argument
sambamba_depth_mapping_quality:
associated_recipe:
- sambamba_depth
data_type: SCALAR
default: 10
type: recipe_argument
sambamba_depth_quality_control:
associated_recipe:
- sambamba_depth
data_type: SCALAR
default: 1
type: recipe_argument
smncopynumbercaller:
analysis_mode: case
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: _smn
outfile_suffix: ".tsv"
program_executables:
- smn_caller.py
type: recipe
star_caller:
analysis_mode: case
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: _cyp2d6
outfile_suffix: ".tsv"
program_executables:
- star_caller.py
type: recipe
telomerecat_ar:
analysis_mode: case
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: _tel
outfile_suffix: ".csv"
program_executables:
- telomerecat
type: recipe
telomerecat_use_sample_id_as_display_name:
associated_recipe:
- telomerecat_ar
data_type: SCALAR
default: 0
type: mip
tiddit_coverage:
analysis_mode: sample
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: _tcov
outfile_suffix: ".wig"
program_executables:
- TIDDIT.py
type: recipe
picardtools_collectmultiplemetrics:
analysis_mode: sample
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: _collectmultiplemetrics
type: recipe
picardtools_collecthsmetrics:
analysis_mode: sample
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: _collecthsmetrics
type: recipe
## Structural Variant Calling
cnvnator_ar:
analysis_mode: sample
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: _cnvnator
outfile_suffix: ".vcf"
program_executables:
- bcftools
- cnvnator
- cnvnator2VCF.pl
- samtools
recipe_type: structural_variant_callers
type: recipe
variant_caller: cnvnator
cnv_bin_size:
associated_recipe:
- cnvnator_ar
data_type: SCALAR
default: 1000
type: recipe_argument
delly_call:
analysis_mode: sample
associated_recipe:
- mip
data_type: SCALAR
default: 0
file_tag: _dellycall
program_executables:
- delly
outfile_suffix: ".bcf"
type: recipe
delly_reformat:
analysis_mode: case
associated_recipe:
- mip
data_type: SCALAR
default: 0
file_tag: _dellyreformat
program_executables:
- delly
- bcftools
outfile_suffix: ".vcf"
recipe_type: structural_variant_callers
type: recipe
variant_caller: delly
delly_exclude_file:
associated_recipe:
- delly_call
- delly_reformat
data_type: SCALAR
default: hg19_human_excl_-20200310-.tsv
exists_check: file
is_reference: 1
reference: reference_dir
type: path
delly_types:
associated_recipe:
- delly_call
- delly_reformat
data_type: ARRAY
default:
- DEL
- DUP
- INV
- INS
type: recipe_argument
expansionhunter:
analysis_mode: case
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: _exphun
outfile_suffix: ".vcf"
program_executables:
- ExpansionHunter
- stranger
recipe_type: repeats_variant_callers
type: recipe
variant_caller: expansionhunter
expansionhunter_variant_catalog_file_path:
associated_recipe:
- expansionhunter
data_type: SCALAR
default: grch37_expansionhunter_variant_catalog_-3.1.2-.json
exists_check: file
is_reference: 1
reference: reference_dir
type: path
update_path: absolute_path
manta:
analysis_mode: case
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: _manta
program_executables:
- configManta.py
outfile_suffix: ".vcf"
recipe_type: structural_variant_callers
type: recipe
variant_caller: manta
manta_call_regions_file_path:
associated_recipe:
- manta
data_type: SCALAR
exists_check: file
is_reference: 1
mandatory: no
reference: reference_dir
type: path
tiddit:
analysis_mode: case
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: _tiddit
outfile_suffix: ".vcf"
coverage_file_suffix: ".tab"
program_executables:
- TIDDIT.py
recipe_type: structural_variant_callers
type: recipe
variant_caller: tiddit
tiddit_coverage_bin_size:
associated_recipe:
- tiddit
- tiddit_coverage
- vcf2cytosure_ar
data_type: SCALAR
default: 500
type: recipe_argument
tiddit_minimum_number_supporting_pairs:
associated_recipe:
- tiddit
data_type: SCALAR
default: 6
type: recipe_argument
sv_combinevariantcallsets:
analysis_mode: case
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: _comb
outfile_suffix: ".vcf"
program_executables:
- bcftools
- vt
type: recipe
sv_combinevariantcallsets_bcf_file:
associated_recipe:
- sv_combinevariantcallsets
data_type: SCALAR
default: 1
type: recipe_argument
sv_svdb_merge_prioritize:
associated_recipe:
- sv_combinevariantcallsets
data_type: SCALAR
default: tiddit,cnvnator,manta
type: recipe_argument
sv_vt_decompose:
associated_recipe:
- sv_combinevariantcallsets
data_type: SCALAR
default: 1
type: recipe_argument
sv_annotate:
analysis_mode: case
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: _ann
outfile_suffix: ".vcf"
program_executables:
- bcftools
- svdb
type: recipe
sv_fqa_annotations:
associated_recipe:
- sv_annotate
data_type: ARRAY
default:
- GNOMADAF
- GNOMADAF_POPMAX
type: recipe_argument
sv_bcftools_view_filter:
associated_recipe:
- sv_annotate
data_type: SCALAR
default: 1
type: recipe_argument
sv_frequency_filter:
associated_recipe:
- sv_annotate
data_type: SCALAR
default: 1
type: recipe_argument
sv_svdb_query:
associated_recipe:
- sv_annotate
data_type: SCALAR
default: 1
type: recipe_argument
sv_svdb_query_db_files:
associated_recipe:
- sv_annotate
data_type: HASH
exists_check: file
is_reference: 1
reference: reference_dir
type: path
sv_vcfanno_config:
associated_recipe:
- sv_annotate
data_type: SCALAR
exists_check: file
is_reference: 1
reference: reference_dir
type: path
vcf2cytosure_ar:
analysis_mode: case
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: _cyto
outfile_suffix: ".cgh"
program_executables:
- bcftools
- TIDDIT.py
- vcf2cytosure
type: recipe
vcf2cytosure_blacklist:
associated_recipe:
- vcf2cytosure_ar
data_type: SCALAR
exists_check: file
is_reference: 1
mandatory: no
reference: reference_dir
type: path
vcf2cytosure_exclude_filter:
associated_recipe:
- vcf2cytosure_ar
data_type: SCALAR
default: "'clingen_ngiAF > 0.1 || swegenAF > 0.05 || clinical_genomics_mipAF > 0.05 || decipherAF > 0.1'"
type: recipe_argument
vcf2cytosure_freq:
associated_recipe:
- vcf2cytosure_ar
data_type: SCALAR
default: 0.01
type: recipe_argument
vcf2cytosure_freq_tag:
associated_recipe:
- vcf2cytosure_ar
data_type: SCALAR
default: FRQ
type: recipe_argument
vcf2cytosure_maxbnd:
associated_recipe:
- vcf2cytosure_ar
data_type: SCALAR
default: 5000
type: recipe_argument
vcf2cytosure_no_filter:
associated_recipe:
- vcf2cytosure_ar
data_type: SCALAR
default: 0
type: recipe_argument
vcf2cytosure_var_size:
associated_recipe:
- vcf2cytosure_ar
data_type: SCALAR
default: 5000
type: recipe_argument
vcf2cytosure_use_sample_id_as_display_name:
associated_recipe:
- vcf2cytosure_ar
data_type: SCALAR
default: 0
type: mip
sv_varianteffectpredictor:
analysis_mode: case
associated_recipe: