Workflow: GATK-Sub-Workflow-h3abionet-indel-no-vqsr.cwl

Fetched 2023-01-11 22:54:17 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
filter_expression String
filter_output_filename String
select_output_filename String

Steps

ID Runs Label Doc
filter_indels
../../tools/GATK-VariantFiltration.cwl (CommandLineTool)

GATK-VariantsFiltration.cwl is developed for CWL consortium

Usage: ``` java -Xmx8G \ -jar gatk.jar -T VariantFiltration \ -R reference.fa \ -V raw_indels.vcf \ --filterExpression \"QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0\" \ --filterName \"my_indel_filter\" \ -o filtered_indels.vcf ```

select_indels
../../tools/GATK-SelectVariants.cwl (CommandLineTool)

GATK-SelectVariants.cwl is developed for CWL consortium

Usage: ``` java -Xmx8G \ -jar gatk.jar -T SelectVariants \ -R reference.fa \ -V raw_HC_variants.vcf \ -selectType INDEL \ -o raw_indels.vcf ```

snpeff_indels
../../tools/snpEff.cwl (CommandLineTool)

Outputs

ID Type Label Doc
annotated_indels File
html json turtle jsonld rdfxml svg png dot zip ro yaml raw
Permalink: https://w3id.org/cwl/view/git/38f5f9618ce651ac9533b4ee09bda6fb0a2dc795/workflows/GATK/GATK-Sub-Workflow-h3abionet-indel-no-vqsr.cwl