Workflow: GATK-Sub-Workflow-h3abionet-snp.cwl

Fetched 2023-01-11 22:57:44 GMT
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Inputs

ID Type Title Doc
snp_mode String
reference File

reference human genome file
indel_mode String
snpf_genome String
haplotest_vcf File
resource_omni File
snpf_data_dir Directory
resource_dbsnp File
resource_mills File
resource_hapmap File
snpf_nodownload Boolean

Steps

ID Runs Label Doc
vqsr_snps
../../tools/GATK-VariantRecalibrator-SNPs.cwl (CommandLineTool)

GATK-VariantsRecalibrator.cwl is developed for CWL consortium

Usage: ``` java -Xmx8G \ -jar gatk.jar -T VariantRecalibrator \ -R [reference_fasta] \ -recalFile $tmpDir/out.recal \ -tranchesFile $tmpDir/out.tranches \ -rscriptFile $tmpDir/out.R \ -nt 4 \ -an MQRankSum -an ReadPosRankSum -an DP -an FS -an QD \ -mode SNP \ -resource:hapmap,known=false,training=true,truth=true,prior=15.0 [hapmap_vcf] \ -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 [dbsnp_vcf] \ -resource:omni,known=false,training=true,truth=true,prior=12.0 [1komni_vcf] \ -resource:1000G,known=false,training=true,truth=false,prior=10.0 [1ksnp_vcf] ```

snpeff_snps
../../tools/snpEff.cwl (CommandLineTool)
apply_recalibration_snps
../../tools/GATK-ApplyRecalibration.cwl (CommandLineTool)

Outputs

ID Type Label Doc
recal_File File
annotated_snps File
html json turtle jsonld rdfxml svg png dot zip ro yaml raw
Permalink: https://w3id.org/cwl/view/git/8e841da119480fdc626dedca572e55d15f9b017f/workflows/GATK/GATK-Sub-Workflow-h3abionet-snp.cwl