Hi, I'm using GATK 188.8.131.52 for Germline and Rare copy number variant discovery.
I have a big dataset of more than 400 samples and I'm studying about 800 genes in each sample. I ran CNV pipeline successfully but unfortunately problem is to handle data at PostprocessGermlineCNVCalling stage. Because this tool give results for only 1 sample at a moment. Is there any way to make multi-sample VCF rather than making separate VCF file for each sample? Just like GenomicsDBImport!
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