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gatk4-genome-processing-pipeline

- This repo has been archived, the workflows new repository location is broadinstitute/warp

Workflows used for germline processing in whole genome sequence data.

WholeGenomeGermlineSingleSample :

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 sequencing data.

Requirements/expectations

  • Human whole-genome paired-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
  • Reference genome must be Hg38 with ALT contigs

Outputs

  • Cram, cram index, and cram md5
  • GVCF and its gvcf index
  • BQSR Report
  • Several Summary Metrics

Software version requirements :

  • GATK 4.0.10.1 and GATK 3.5
  • By default, HaplotypeCaller will perform variant calling using GATK 3.5, which is what is used in Broad Production. To use GATK4, specify use_gatk3_haplotype_caller=false in the inputs.json.
  • Picard 2.20.0-SNAPSHOT
  • Samtools 1.3.1
  • Python 2.7
  • Cromwell version support
    • Successfully tested on v53

Important Notes :

  • The provided JSON is a generic ready to use example template for the workflow. It is the user’s responsibility to correctly set the reference and resource variables for their own particular test case using the GATK Tool and Tutorial Documentations.
  • Runtime parameters are optimized for Broad's Google Cloud Platform implementation.
  • For help running workflows on the Google Cloud Platform or locally please view the following tutorial (How to) Execute Workflows from the gatk-workflows Git Organization.
  • Please visit the User Guide site for further documentation on our workflows and tools.
  • Relevant reference and resources bundles can be accessed in Resource Bundle.

Contact Us :

  • The following material is provided by the Data Science Platforum group at the Broad Institute. Please direct any questions or concerns to one of our forum sites : GATK or Terra.

LICENSING :

Copyright Broad Institute, 2020 | BSD-3 This script is released under the WDL open source code license (BSD-3) (full license text at https://github.com/openwdl/wdl/blob/master/LICENSE). Note however that the programs it calls may be subject to different licenses. Users are responsible for checking that they are authorized to run all programs before running this script.