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germline_varcall.yaml
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germline_varcall.yaml
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---
info:
name: "Germline_variant_calling"
desc: "Lars Birger Aasheim"
log_dir: "output/Logs"
steps_status_dir: "output/FinishedSteps"
workflow_steps:
#
# Germline variant Calling
#
-
tool: "GATK_HaplotypeCaller"
id: "GATK_HaplotypeCaller_loop"
desc: "Call Variants from Bam"
depend_from: ""
step_options:
input_dir: "output/04_gatk_recal"
input_files: "*.bam"
output_dir: "output/11_Haplotypes"
output_suffix: "haplotype"
gatk_jar: "/Jar/GenomeAnalysisTK.jar"
core: 8 # This is a risky setting due to a random crash risk. Use at your own risk. Values over 8 are often detrimental to performance.
java_bin: "java"
ref_path: "references/human_g1k_v37_decoy.fasta"
command_line_options:
java:
- "-Xmx15G"
- "-Djava.io.tmpdir=/tmp"
gatk:
- ""
gatk_HaplotypeCaller:
- "--emitRefConfidence GVCF "
- "--variant_index_type LINEAR "
- "--variant_index_parameter 128000 "
- "-XL hs37d5"
#
# Merging
#
-
tool: "GATK_GenotypeGVCFs"
id: "GATK_GenotypeGVCFs"
desc: "Merge all VCF"
depend_from: ["GATK_HaplotypeCaller_loop"]
step_options:
input_dir: "output/11_Haplotypes"
input_files: "*.vcf"
output_dir: "output/12_Genotypes"
output_suffix: "_haplotype"
gatk_jar: "/Jar/GenomeAnalysisTK.jar"
core: 16
java_bin: "java"
ref_path: "references//human_g1k_v37_decoy.fasta"
command_line_options:
java:
- "-Xmx15G"
- "-Djava.io.tmpdir=/tmp"
gatk:
- ""
gatk_GVCF:
- ""
#
# Recalibration
#
-
tool: "GATK_VariantRecalibratorApplied"
id: "GATK_VariantRecalibratorApplied_INDEL"
desc: "Variant Recalibration for Indels"
depend_from: ["GATK_GenotypeGVCFs"]
result: "true"
step_options:
input_dir: "output/12_Genotypes"
input_files: "*.vcf"
output_dir: "output/13_variants_INDELs"
output_suffix: "INDEL"
gatk_jar: "/Jar/GenomeAnalysisTK.jar"
core: 16
java_bin: "java"
ref_path: "references//human_g1k_v37_decoy.fasta"
mode: "INDEL"
command_line_options:
java:
- "-Xmx15G"
- "-Djava.io.tmpdir=/tmp"
gatk:
- ""
gatk_vr:
- "-resource:mills,known=false,training=true,truth=true,prior=12.0 references/Mills_and_1000G_gold_standard.indels.b37.vcf "
- "-resource:dbsnp,known=true,training=false,truth=false,prior=2.0 references/dbsnp.vcf "
- "-an QD -an FS -an SOR -an DP -an ReadPosRankSum -an MQRankSum "
- "-tranche 100.0 -tranche 99.95 -tranche 99.9 -tranche 99.5 -tranche 99.0 -tranche 97.0 -tranche 96.0 -tranche 95.0 -tranche 94.0 "
- "-tranche 93.5 -tranche 93.0 -tranche 92.0 -tranche 91.0 -tranche 90.0 "
- "-mG 4"
gatk_ar:
- "--ts_filter_level 95.0 "
-
tool: "GATK_VariantRecalibratorApplied"
id: "GATK_VariantRecalibratorApplied_SNPs"
desc: "Variant Recalibration for SNPs"
depend_from: ["GATK_GenotypeGVCFs"]
result: "true"
step_options:
input_dir: "output/12_Genotypes"
input_files: "*.vcf"
output_dir: "output/13_variants_SNPs"
output_suffix: "SNPs"
gatk_jar: "/Jar/GenomeAnalysisTK.jar"
core: 16
java_bin: "java"
ref_path: "references//human_g1k_v37_decoy.fasta"
mode: "SNP"
command_line_options:
java:
- "-Xmx15G"
- "-Djava.io.tmpdir=/tmp"
gatk:
- ""
gatk_vr:
- "-resource:omni,known=false,training=true,truth=true,prior=12.0 references/omni.vcf "
- "-resource:1000G,known=false,training=true,truth=false,prior=10.0 references/1000g.vcf "
- "-resource:dbsnp,known=true,training=false,truth=false,prior=2.0 references/dbsnp.vcf "
- "-resource:hapmap,known=false,training=true,truth=true,prior=15.0 references/hapmap.vcf "
- "-an QD -an MQ -an DP -an FS -an SOR -an MQRankSum -an ReadPosRankSum "
- "-tranche 100.0 -tranche 99.95 -tranche 99.9 -tranche 99.8 -tranche 99.6 -tranche 99.5 -tranche 99.4 "
- "-tranche 99.3 -tranche 99.0 -tranche 98.0 -tranche 97.0 -tranche 90.0"
gatk_ar:
- "--ts_filter_level 99.6 "