As of GATK 4.2.3.0 (September 2023), missing genotypes in VCFs are coded as 0/0 instead of ./., and missingness is indicated in the FORMAT DP field.
This is likely a breaking change for mutyper's mutation spectrum processing, so should be assessed and hopefully fixed. It's not clear to me if cyvcf2 (which we use for VCF parsing) has been updated to handle this.
As of GATK 4.2.3.0 (September 2023), missing genotypes in VCFs are coded as
0/0instead of./., and missingness is indicated in the FORMAT DP field.This is likely a breaking change for mutyper's mutation spectrum processing, so should be assessed and hopefully fixed. It's not clear to me if
cyvcf2(which we use for VCF parsing) has been updated to handle this.See: https://gatk.broadinstitute.org/hc/en-us/articles/6012243429531-GenotypeGVCFs-and-the-death-of-the-dot