ALLELE_A and ALLELE_B encoding in the VCF?

[rajwanir]

Hi @freeseek ,

What does 0 and 1 represent for ALLELE_A and ALLELE_B in the VCF INFO?

It seems like the Picard tools GtcToVcf implementation write alleles themselves in the Allele A and Alllele B place?https://github.com/search?q=repo%3Abroadinstitute%2Fpicard%20getAlleleA&type=code

I wanted to convert the VCF to adpc.bin throught the Picard tools to run through VerifyIDintensity (https://github.com/gjun/verifyIDintensity) for contamination checks and noted some inconsistency/incompatiblity. Do you have any thoughts?

Thanks.