Unexpected output using SelectVariants
Firstly, SelectVariants is an awesome feature to subset out samples very fast out of a large bcf/vcf.
I am subsetting samples out of a bigger bcf/vcf using the --excludeNonVariants and --keepOriginalAC with -sf option.
I noticed when the source vcf is multi-allelic and the resulting subset becomes bi-allelic two things are non-ideal
- AC_Orig, AF_Orig and AN_Orig tags have more than one value and it is ambiguous which one refers to the ALT in the new vcf
- The AD and PL values are now missing for the individual sample genotypes
Is there an option I can use to get around this?