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gatk-somatic-with-preprocessing

This WDL pipeline implements data pre-processing and initial calling for somatic SNP, Indel, and copy number variants in human whole-genome sequencing (WGS) data.

Note: The gatk-somatic-with-preprocessing WDL is not used in any pipelines at the Broad Institute
and has been provided only as a convenience for the community. Therefore, this WDL is unsupported.

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
  • Reference genome must be Hg38 with ALT contigs

Runtime parameters are optimized for Broad's Google Cloud Platform implementation. For program versions, see docker containers.

Software version requirements :

Cromwell version support

  • Successfully tested on v30.2
  • Does not work on versions < v30 due to output syntax

LICENSING :

This script is released under the WDL source code license (BSD-3) (see LICENSE in https://github.com/broadinstitute/wdl). 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. Please see the docker page at https://hub.docker.com/r/broadinstitute/genomes-in-the-cloud/ for detailed licensing information pertaining to the included programs.