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
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
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