gatk3-data-processing

GATK3 and this workflow is now longer supported, this repo is intended for legacy purposes.

Purpose :

Workflows for processing high-throughput sequencing data for variant discovery with GATK3 and related tools

processing-for-variant-discovery-gatk3 :

The processing-for-variant-discovery-gatk3 WDL pipeline implements data pre-processing according to the GATK Best Practices (June 2016).

Requirements/expectations

• 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

Outputs

• A clean BAM file and its index, suitable for variant discovery analyses.

Software version requirements :

• GATK 3
• Picard 2.x
• Samtools (see gotc docker)
• Python 2.7

Cromwell version support

• Successfully tested on v33
• Does not work on versions < v23 due to output syntax

Runtime parameters are optimized for Broad's Google Cloud Platform implementation.