gatk4-data-processing

Purpose :

Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools.

processing-for-variant-discovery-gatk4 :

The processing-for-variant-discovery-gatk4 WDL pipeline implements data pre-processing according to the GATK Best Practices (June 2016). Example JSONs are provided for the WGS use case but the workflow can be applied to Exomes and Targeted Panels.

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 4.beta.3 or later
• Picard 2.x
• Samtools (see gotc docker)
• Python 2.7

Cromwell version support

• Successfully tested on v28
• Does not work on versions < v23 due to output syntax

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