dayedepps / five-dollar-genome-analysis-pipeline

Workflows used for germline short variant discovery in WGS data

five-dollar-genome-analysis-pipeline

Workflows used for germline short variant discovery in WGS data

germline_single_sample_workflow :

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.

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 :

Cromwell version support

• Successfully tested on v30.2
• Does not work on versions < v23 due to output syntax