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.
How to includeing loci of non-variant in GenotypeGVCFs step with GATK4?
I called germline short variants using haplotype caller with GATK 4.0, and then I want to extracted the non-variants and variants ** into seperate files so I could filter them seperately. In the GATK 3.x pipeline, there used to be **-allSites or --includeNonVariantSites in GenotypeGVCFs . Is it there no more in this new version?
Thanks in advance~