How to distinguish homozygous Reference with Missing genotype after merging multiple

[jdpr_100]

The SNPs were called for each individual and multiple VCF files were combined. Is it a way to find out missing genotypes and checks if it is homozygous Reference or no-called site after merging multiple VCF files?
Thanks in advance for your help.

[dickie_ho]

Hey mate

Check this out https://github.com/lindenb/jvarkit/w...ssingGenotypes

haven't used it yet myself, just regenerating all my bam files again because I ran into the same issue

Cheers

Josh