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Old 08-15-2018, 11:01 AM   #1
htetre
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Default PL high support for each GT for all SNPS

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
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Old 08-16-2018, 09:55 PM   #2
SNPsaurus
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I haven't seen that error before. Were both bam files sorted? Can you make a vcf file for each sample?
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Old 08-20-2018, 12:05 PM   #3
htetre
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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.
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