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Broad WGS Single Sample pipeline

Version:
v2.3.1
Identifier: WF_63e0c3.bc

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Overview

This WDL pipeline implements data pre-processing and initial variant calling (GVCF generation) according to the GATK Best Practices (June 2016) for germline SNP and Indel discovery in human whole-genome data Requirements/expectations : - Human whole-genome pair-end sequencing data in unmapped BAM (uBAM) format - One or more read groups, one per uBAM file, all belonging to a single sample (SM) - Input uBAM files must additionally comply with the following requirements - - filenames all have the same suffix (we use ".unmapped.bam") - - files must pass validation by ValidateSamFile - - reads are provided in query-sorted order - - all reads must have an RG tag - GVCF output names must end in ".g.vcf.gz" - Reference genome must be Hg38 with ALT contigs

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  • WARP Plumbing GATK SS Test

    Official test data from https://raw.githubusercontent.com/broadinstitute/warp/develop/pipelines/broad/dna_seq/germline/single_sample/wgs/input_files/WholeGenomeGermlineSingleSample.inputs.plumbing.json

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  • WARP Plumbing GATK SS Test

    Official test data from https://raw.githubusercontent.com/broadinstitute/warp/develop/pipelines/broad/dna_seq/germline/single_sample/wgs/input_files/WholeGenomeGermlineSingleSample.inputs.plumbing.json

     0
  • WARP Plumbing GATK SS Test Public

    Official test data from https://raw.githubusercontent.com/broadinstitute/warp/develop/pipelines/broad/dna_seq/germline/single_sample/wgs/input_files/WholeGenomeGermlineSingleSample.inputs.plumbing.json

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