problems about vcfm2acf about glactools HOT 2 OPEN

Hello! Thank you for your interest in my software! My apologies for the delay in replying I'm currently on paternity leave.

This is not really a bug, it is more like a feature. I did not expect that it caller would simultaneously produce PL and GL. It does not make much sense. If I had more time I could add a flag to accept such format. However, I have very little time during the day.

Could you try to modify the input file to remove the pl field?

from glactools.

Thanks for your reply! I used bcftools to remove the PL field. And after I did so, the glactools began to work successfully. I'll put my code here to help others who may encounter the similar problems. And you can close this issue. Thanks one more time.

bcftools view --header-only chr22.vcf.gz >> chr22.vcf
bcftools query -f '%CHROM\t%POS\t%ID\t%REF\t%ALT\t%QUAL\t%FILTER\t%INFO\tGT:GQ:DP:AD:VAF:GL[\t%GT:%GQ:%DP:%AD:%VAF:%GL]\n' chr22.vcf.gz >> chr22.vcf

from glactools.