Open mr-c opened 3 years ago
I would suggest the GATK workflow --
List of different versions: https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels-
I would start either with the $5 version probably
$5 has moved to here: https://github.com/broadinstitute/warp/tree/develop/pipelines/broad/dna_seq/germline/single_sample/wgs
Also, other pipelines in WARP might be useful ---> https://github.com/broadinstitute/warp
Here are some WDL examples that toil-wdl-runner uses: http://toil-datasets.s3.amazonaws.com/wdl_templates.zip