PL high support for each GT for all SNPS

[htetre]

Hello,

I have two populations I am trying to discover SNPs for. In my .vcf file one population has the GT and the PL is 0,0,0 for every single snp ie 0/1, 0/0, and 1/1. Does anyone know where I went wrong? My sam to bam conversion shrunk my data file considerably (179G to 27G) compared to the second pooled population (173G to 46G) in this study. Other than that I cant seem to pinpoint a difference in my two samples.

Thank you for any and all help

[SNPsaurus]

I haven't seen that error before. Were both bam files sorted? Can you make a vcf file for each sample?

[htetre]

I am currently trying to call SNPs with the problematic file alone. I am able to get expected results, ie high support for one GT and low support for the other two GT with the "non-problematic" file.