vcztools drops FORMAT fields with missing values when subsetting samples, instead of emitting . placeholders like bcftools
When subsetting chr22.vcf.gz to a single sample (-s HG00096), vcztools omits FORMAT fields where the selected sample has no data, while bcftools retains them with . placeholders.
bcftools: GT:AD:DP:GQ:PL ./.:0,0:0:.:.
vcztools: AD:DP 0,0:0
This causes downstream tools (e.g. cyvcf2) to fail when they expect GT to be present.
I think this is a bug, because we can't have AD/DP with no GT.
vcztools drops FORMAT fields with missing values when subsetting samples, instead of emitting . placeholders like bcftools
When subsetting chr22.vcf.gz to a single sample (-s HG00096), vcztools omits FORMAT fields where the selected sample has no data, while bcftools retains them with . placeholders.
This causes downstream tools (e.g. cyvcf2) to fail when they expect GT to be present.
I think this is a bug, because we can't have AD/DP with no GT.