User: goatsrunfaster

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Posts by goatsrunfaster

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Identify unique SNPs specific to pre-defined clades or clusters across large data-set
... I'm looking to identify SNPs unique to specific pre-defined clades or clusters across a large bacterial WGS data-set. I am able to do this manually by loading my .vcf file with my .fasta reference into Gingr (with my tree), but scrolling across 5 million reads is giving me a headache. Anyone know of ...
genome alignment snp written 21 days ago by goatsrunfaster0
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Answer: A: Lositan, He and Microsats (expected heterozygosity measures plot higher than exp
... found the answer in another post: "In Lositan the Heterozygosity is h_b rather than h_t - i.e. it is the probability of choosing two alleles at random that are different, one from each deme, rather than the prob of picking two alleles at random that are different irrespective of deme. With two dem ...
written 2.7 years ago by goatsrunfaster0
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Lositan, He and Microsats (expected heterozygosity measures plot higher than expected)
... When I load my data into Lositan, the loci plot at higher He than expected given the measures produced by Arlequin and Genepop. Does Lositan not plot the mean He for each loci, or is this another measure of He (an upper quartile or something)? I checked another paper that provides a lositan output, ...

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