The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
Set up pipeline for WES and WGS
working with WES and WGS data (GATK 220.127.116.11) I would like to know the set up differents between their pipelines for germline and somatic variant discovery.
I saw that I have to use two different interval lists (-L, BQSR & HC), as also in the VQSR step I have to exclude the -an DP option in the WES pipeline .
Moreover, in the site it is reported that there is a WES pipeline with hg19 and a WGS pipeline with hg38, in which the last one is in the Best Practices pages.
Could you provide me any link about the WES set up.