Is it possible to run GATK4 with HG37 data?
You may want to review the Best Practices page which describes the step-by-step recommendations for performing variant discovery. Also on the left are links to different analysis phases, for example Data Preprocessing and Germline SNP+INDEL . Within these analysis phase web pages are links to example workflows listed under "Reference Implementation".
Sorry I meant GRCh37 / hg19 (not sure where to modify the post above).
So I'd need to find (or create) a WDL that runs Whole-Genome Sequencing with GRCh37 / hg19 data. Would you know any - or could you point me to a correct library and command to do this?
Will do, thanks.