Remove variants from merged VCF file - CombineVariants
I used GATK to merge two VCF files using CombineVariants tool. In the downstream analysis (in Minimac3) I get following error:
Missing Value for Individual : GS000019695-ASM at Marker : 1:47267
Is there an option in CombineVariants or SelectVariants to exclude markers that are missing in one file?
Thank you very much.