Workflows used for germline short variant discovery in WGS data
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 and exome sequencing data. The provided intervals in the json are intended for whole-genome sequencing, users are expected to use thier own exome intervals for exome sequencing.
Note: For those users interested in running this wdl on FireCloud (FC), the FC version has been provided as fc_germline_single_sample_workflow.wdl. Please visit the FC featured methods and workspaces for more GATK Best Practices pipelines.
- 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:
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- filenames all have the same suffix (we use ".unmapped.bam")
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- files must pass validation by ValidateSamFile
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- reads are provided in query-sorted order
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- all reads must have an RG tag
- Reference genome must be Hg38 with ALT contigs
- Cram, cram index, and cram md5
- GVCF and its gvcf index
- BQSR Report
- Several Summary Metrics
Cromwell version support
- Successfully tested on v30.2
- Does not work on versions < v23 due to output syntax