Workflow: Whole Exome Sequencing

Fetched 2023-01-03 19:26:01 GMT

Whole Exome Sequence analysis using GATK best practices - Germline SNP & Indel Discovery

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Inputs

ID Type Title Doc
GATKJar File
library String
threads Integer (Optional)
platform String
intervals File[] (Optional)
knownSites File[]
read_pairs https://w3id.org/cwl/view/git/ef08cb00bd55b4c712645d171dbc691e01ed6165/packed/exomeseq.cwl#bespin-types.yml/NamedFASTQFilePairType[]
study_type https://w3id.org/cwl/view/git/ef08cb00bd55b4c712645d171dbc691e01ed6165/packed/exomeseq.cwl#bespin-types.yml/ExomeseqStudyType
resource_dbsnp File
interval_padding Integer (Optional)
reference_genome File
snp_resource_1kg File
primary_intervals File[] (Optional)
snp_resource_omni File
snp_resource_hapmap File
indel_resource_mills File

Steps

ID Runs Label Doc
preprocessing
variant_discovery
organize_directories
prepare_reference_data

Outputs

ID Type Label Doc
bams_final_dir Directory

BAM files containing assembled haplotypes and locally realigned reads

hs_metrics_dir Directory
raw_variants_dir Directory
trim_reports_dir Directory
fastqc_reports_dir Directory
joint_raw_variants File

GVCF file from joint genotyping calling

bams_markduplicates_dir Directory

BAM and bai files from markduplicates

filtered_recalibrated_variants File

The output filtered and recalibrated VCF file in which each variant is annotated with its VQSLOD value

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