/
rd_dna_panel_parameters.yaml
executable file
·1242 lines (1242 loc) · 26.2 KB
/
rd_dna_panel_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
- 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
- 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
- gatk_baserecalibration
- gatk_haplotypecaller
- gatk_genotypegvcfs
- gatk_variantevalall
- gatk_variantevalexome
- gatk_variantrecalibration
- mip
- picardtools_collecthsmetrics
- picardtools_collectmultiplemetrics
- 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
- gatk_baserecalibration
- gatk_haplotypecaller
- gatk_genotypegvcfs
- gatk_variantevalall
- gatk_variantevalexome
- gatk_variantrecalibration
- picardtools_collecthsmetrics
- picardtools_collectmultiplemetrics
- 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: 12
bwa_mem2: 12
cadd_ar: 1
endvariantannotationblock: 1
fastqc_ar: 0
variant_annotation: 1
frequency_filter: 1
gatk_baserecalibration: 1
gatk_combinevariantcallsets: 1
gatk_gathervcfs: 1
gatk_genotypegvcfs: 1
gatk_haplotypecaller: 1
gatk_variantevalall: 1
gatk_variantevalexome: 1
gatk_variantrecalibration: 1
gzip_fastq: 0
markduplicates: 1
multiqc_ar: 1
picardtools_collecthsmetrics: 1
picardtools_collectmultiplemetrics: 1
qccollect_ar: 1
rtg_vcfeval: 36
sacct: 1
sambamba_depth: 1
samtools_merge: 2
varianteffectpredictor: 1
vcfparser_ar: 1
version_collect_ar: 1
vt_ar: 1
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: 4
endvariantannotationblock: 2
variant_annotation: 3
gatk_baserecalibration: 10
gatk_gathervcfs: 7
gatk_genotypegvcfs: 12
gatk_variantrecalibration: 30
markduplicates: 10
picardtools_collecthsmetrics: 8
picardtools_collectmultiplemetrics: 8
sambamba_depth: 10
varianteffectpredictor: 7
vcfparser_ar: 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: 2
bwa_mem2: 2
cadd_ar: 2
endvariantannotationblock: 1
fastqc_ar: 10
variant_annotation: 1
frequency_filter: 1
gatk_baserecalibration: 5
gatk_combinevariantcallsets: 2
gatk_genotypegvcfs: 10
gatk_gathervcfs: 2
gatk_haplotypecaller: 10
gatk_variantevalall: 2
gatk_variantevalexome: 2
gatk_variantrecalibration: 10
gzip_fastq: 2
markduplicates: 5
multiqc_ar: 5
picardtools_collecthsmetrics: 5
picardtools_collectmultiplemetrics: 5
qccollect_ar: 1
rankvariant: 1
rtg_vcfeval: 1
sacct: 1
sambamba_depth: 1
samtools_merge: 2
varianteffectpredictor: 4
vcfparser_ar: 1
version_collect_ar: 1
vt_ar: 2
vt_core: 2
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
- picardtools_collecthsmetrics
- picardtools_collectmultiplemetrics
data_type: SCALAR
type: path
### Programs
## 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
## 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
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
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
## GATK Genotype
gatk_haplotypecaller:
analysis_mode: sample
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: _haptc
outfile_suffix: ".vcf"
program_executables:
- gatk
type: recipe
gatk_haplotypecaller_annotation:
associated_recipe:
- gatk_haplotypecaller
data_type: ARRAY
default:
- BaseQualityRankSumTest
- ChromosomeCounts
- Coverage
- DepthPerAlleleBySample
- FisherStrand
- MappingQualityRankSumTest
- QualByDepth
- RMSMappingQuality
- ReadPosRankSumTest
- StrandOddsRatio
type: recipe_argument
# BaseQualityRankSumTest; #Rank Sum Test of REF versus ALT base quality scores
# ChromosomeCounts; #Counts and frequency of alleles in called genotypes
# Coverage; #Total depth of coverage per sample and over all samples
# DepthPerAlleleBySample; #Depth of coverage of each allele per sample
# FisherStrand; #Strand bias estimated using Fisher's Exact Test
# MappingQualityRankSumTest; #Rank Sum Test for mapping qualities of REF versus ALT reads
# QualByDepth; #Variant confidence normalized by unfiltered depth of variant samples
# RMSMappingQuality; #Root Mean Square of the mapping quality of reads across all samples
# ReadPosRankSumTest; #Rank Sum Test for relative positioning of REF versus ALT alleles within reads
# StrandOddsRatio ; #Strand bias estimated by the Symmetric Odds Ratio test
gatk_haplotypecaller_emit_ref_confidence:
associated_recipe:
- gatk_haplotypecaller
data_type: SCALAR
default: "GVCF"
type: recipe_argument
gatk_haplotypecaller_no_soft_clipped_bases:
associated_recipe:
- gatk_haplotypecaller
data_type: SCALAR
default: 1
type: recipe_argument
gatk_haplotypecaller_pcr_indel_model:
associated_recipe:
- gatk_haplotypecaller
data_type: SCALAR
default: "CONSERVATIVE"
type: recipe_argument
gatk_haplotypecaller_snp_known_set:
associated_recipe:
- gatk_haplotypecaller
data_type: SCALAR
default: grch37_dbsnp_-138-.vcf
exists_check: file
is_reference: 1
reference: reference_dir
type: path
## GATK Genotype Calibration
gatk_genotypegvcfs:
analysis_mode: case
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: _gent
outfile_suffix: ".vcf"
program_executables:
- gatk
type: recipe
gatk_genotypegvcfs_ref_gvcf:
associated_recipe:
- gatk_genotypegvcfs
data_type: SCALAR
exists_check: file
is_reference: 1
reference: reference_dir
type: path
gatk_genotypegvcfs_all_sites:
associated_recipe:
- gatk_genotypegvcfs
data_type: SCALAR
default: 0
type: recipe_argument
gatk_gathervcfs:
analysis_mode: case
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: ""
outfile_suffix: ".vcf"
program_executables:
- bcftools
- gatk
type: recipe
gatk_gathervcfs_bcf_file:
associated_recipe:
- gatk_gathervcfs
data_type: SCALAR
default: 0
type: recipe_argument
gatk_variantrecalibration:
analysis_mode: case
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: _vrecal
program_executables:
- bcftools
- gatk
recipe_type: variant_callers
outfile_suffix: ".vcf"
type: recipe
variant_caller: haplotypecaller
gatk_calculategenotypeposteriors:
associated_recipe:
- gatk_variantrecalibration
data_type: SCALAR
default: 0
type: recipe_argument
gatk_cnnscorevariants:
associated_recipe:
- gatk_variantrecalibration
data_type: SCALAR
default: 0
type: recipe_argument
# Connected to AN / 2 for gatk_calculate_genotype_call_set
gatk_num_reference_samples_if_no_call:
associated_recipe:
- gatk_variantrecalibration
data_type: SCALAR
default: 7854
type: recipe_argument
gatk_calculate_genotype_call_set:
associated_recipe:
- gatk_variantrecalibration
data_type: SCALAR
default: grch37_gnomad.genomes_-r2.0.1-.vcf.gz
exists_check: file
is_reference: 1
reference: reference_dir
type: path
gatk_variantrecalibration_annotations:
associated_recipe:
- gatk_variantrecalibration
data_type: ARRAY
default:
- QD
- MQ
- MQRankSum
- ReadPosRankSum
- FS
- SOR
- DP
type: recipe_argument
gatk_variantrecalibration_dp_annotation:
associated_recipe:
- gatk_variantrecalibration
data_type: SCALAR
default: 1
type: recipe_argument
gatk_variantrecalibration_indel_max_gaussians:
associated_recipe:
- gatk_variantrecalibration
data_type: SCALAR
default: 1
type: recipe_argument
gatk_variantrecalibration_indel_tsfilter_level:
associated_recipe:
- gatk_variantrecalibration
data_type: SCALAR
default: 99.99
type: recipe_argument
gatk_variantrecalibration_keep_unnormalised:
associated_recipe:
- gatk_variantrecalibration
data_type: SCALAR
default: 0
type: recipe_argument
gatk_variantrecalibration_resource_indel:
associated_recipe:
- gatk_variantrecalibration
data_type: HASH
default:
grch37_dbsnp_-138-.vcf: "dbsnp,known=true,training=false,truth=false,prior=2.0"
grch37_mills_and_1000g_-gold_standard_indels-.vcf: "mills,known=false,training=true,truth=true,prior=12.0"
exists_check: file
is_reference: 1
reference: reference_dir
type: path
gatk_variantrecalibration_resource_snv:
associated_recipe:
- gatk_variantrecalibration
data_type: HASH
default:
grch37_dbsnp_-138-.vcf: "dbsnp,known=true,training=false,truth=false,prior=2.0"
grch37_hapmap_-3.3-.vcf: "hapmap,known=false,training=true,truth=true,prior=15.0"
grch37_1000g_omni_-2.5-.vcf: "omni,known=false,training=true,truth=truth,prior=12.0"
grch37_1000g_snps_high_confidence_-phase1-.vcf: "1000G,known=false,training=true,truth=false,prior=10.0"
exists_check: file
is_reference: 1
reference: reference_dir
type: path
gatk_variantrecalibration_snv_max_gaussians:
associated_recipe:
- gatk_variantrecalibration
data_type: SCALAR
default: 0
type: recipe_argument
gatk_variantrecalibration_snv_tsfilter_level:
associated_recipe:
- gatk_variantrecalibration
data_type: SCALAR
default: 99.99
type: recipe_argument
gatk_variantrecalibration_ts_tranches:
associated_recipe:
- gatk_variantrecalibration
data_type: ARRAY
default:
- 100
- 99.99
- 99.9
- 99.0
- 90
type: recipe_argument
gatk_variantrecalibration_trust_all_polymorphic:
associated_recipe:
- gatk_variantrecalibration
data_type: SCALAR
default: 0
type: recipe_argument
gatk_combinevariantcallsets:
analysis_mode: case
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: _gatkcomb
outfile_suffix: ".vcf"
type: recipe
gatk_combinevariantcallsets_bcf_file:
associated_recipe:
- gatk_combinevariantcallsets
data_type: SCALAR
default: 1
type: recipe_argument
gatk_combinevariants_genotype_merge_option:
associated_recipe:
- gatk_combinevariantcallsets
data_type: SCALAR
default: PRIORITIZE
mandatory: no
type: recipe_argument
gatk_combinevariants_prioritize_caller:
associated_recipe:
- gatk_combinevariantcallsets
data_type: SCALAR
mandatory: no
type: recipe_argument
## VT
vt_ar:
analysis_mode: case
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: _vt
program_executables:
- vt
- bgzip
- tabix
outfile_suffix: ".vcf"
type: recipe
vt_decompose:
associated_recipe:
- vt_ar
- vt_core
data_type: SCALAR
default: 1
type: recipe_argument
vt_normalize:
associated_recipe:
- vt_ar
- vt_core
data_type: SCALAR
default: 1
type: recipe_argument
vt_missing_alt_allele:
associated_recipe:
- vt_ar
data_type: SCALAR
default: 1
type: recipe_argument
vt_uniq:
associated_recipe:
- vt_ar
- vt_core
data_type: SCALAR
default: 1
type: recipe_argument
vt_core:
analysis_mode: case
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: _vt
program_executables:
- vt
- bgzip
- tabix
type: recipe
variant_annotation:
analysis_mode: case
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: _af
outfile_suffix: ".vcf.gz"
program_executables:
- bcftools
- vcfanno
type: recipe
vcfanno_config:
associated_recipe:
- variant_annotation
data_type: SCALAR
exists_check: file
is_reference: 1
reference: reference_dir
type: path
frequency_filter:
analysis_mode: case
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: _frqf
outfile_suffix: ".vcf.gz"
program_executables:
- bcftools
type: recipe
fqf_annotations:
associated_recipe:
- frequency_filter
data_type: ARRAY
default:
- GNOMADAF
- GNOMADAF_popmax
- SWEGENAF
type: recipe_argument
fqf_bcftools_filter_threshold:
associated_recipe:
- frequency_filter
data_type: SCALAR
default: 0.40
type: recipe_argument
cadd_ar:
analysis_mode: case
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: _cadd
outfile_suffix: ".vcf"
program_executables:
- bcftools
- CADD.sh
type: recipe
cadd_column_names:
associated_recipe:
- cadd_ar
data_type: ARRAY
default:
- Chrom
- Pos
- Ref
- Alt
- "-"
- CADD
type: recipe_argument
cadd_vcf_header_file:
associated_recipe:
- cadd_ar
data_type: SCALAR
default: cadd_to_vcf_header_-1.0-.txt
exists_check: file
is_reference: 1
reference: reference_dir
type: path
gatk_variantevalall:
analysis_mode: sample
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: _evalall
outfile_suffix: ".varianteval"
type: recipe
gatk_variantevalexome:
analysis_mode: sample
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: _evalexome
outfile_suffix: ".varianteval"
program_executables:
- bedtools
type: recipe
gatk_varianteval_dbsnp:
associated_recipe:
- gatk_variantevalall
- gatk_variantevalexome
data_type: SCALAR
default: grch37_dbsnp_-138_esa_129-.vcf
exists_check: file
is_reference: 1
reference: reference_dir
type: path
gatk_varianteval_gold:
associated_recipe:
- gatk_variantevalall
- gatk_variantevalexome
data_type: SCALAR
default: grch37_mills_and_1000g_-gold_standard_indels-.vcf
exists_check: file
is_reference: 1
reference: reference_dir
type: path
## VEP
varianteffectpredictor:
analysis_mode: case
associated_recipe:
- mip
data_type: SCALAR
default: 1
file_tag: _vep
outfile_suffix: ".vcf"
program_executables:
- vep
type: recipe
vep_custom_annotation:
associated_recipe:
- varianteffectpredictor
data_type: HASH
is_reference: 1
mandatory: no
type: path
vep_directory_cache:
associated_recipe:
- varianteffectpredictor
data_type: SCALAR
exists_check: directory
is_reference: 1
type: path
update_path: absolute_path
vep_features:
associated_recipe:
- varianteffectpredictor
data_type: ARRAY
default:
- appris
- biotype
- cache
- canonical
- ccds
- domains
- exclude_predicted
- force_overwrite
- hgvs
- humdiv
- no_progress
- no_stats
- numbers
- merged
- "polyphen p"
- protein
- offline
- regulatory
- "sift p"
- symbol
- tsl
- uniprot
type: recipe_argument
vep_plugin:
associated_recipe:
- varianteffectpredictor
data_type: HASH
is_reference: 1
mandatory: no
type: recipe_argument
vep_plugins_dir_path:
associated_recipe:
- varianteffectpredictor
data_type: SCALAR
exists_check: directory
is_reference: 1
type: path
update_path: absolute_path
## VCFParser
vcfparser_ar:
analysis_mode: case