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calling SNPs with pooled samples using UnifiedGenotyper

jwhitneyjwhitney University of Hawaii Member

I using the UnifiedGenotyper to call SNPs in a pooled sample of 30 diploid individuals (i.e., I am setting the ploidy to 60). Does this mean that if the coverage is < 60 at a given variant site, the vcf file will read "./." for all alleles at that site? In other words, does it require the coverage to be >= the ploidy or it won't produce a called variant at that site? I'm just trying to make sure I am interpreting the vcf file correctly, in that: if there is a called genotype at a given variant site that I can interpret that as the estimated allele frequency in that pool.

Thanks in advance for any advice.

Best,
Jon

Best Answers

Answers

  • jwhitneyjwhitney University of Hawaii Member

    Thank you both very much, you answered my question perfectly

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