Broad WGS Single Sample pipeline

Identifier: WF_63e0c3.bc


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 data 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 - GVCF output names must end in ".g.vcf.gz" - Reference genome must be Hg38 with ALT contigs