User: goatsrunfaster

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Posts by goatsrunfaster

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FORMAT 'PL' is not defined in the header, assuming Type=String (bcftools)
... I am trying to use bcftools to fix references on some older VCF files I have, but I keep getting errors related to the phred-scaled genotype likelihoods (PL). see below: (reddog) -bash-4.2$ bcftools +fixref all.mergedSNPsApril.vcf.gz -- -f Myotis_lucifugus.Myoluc2.0.75.dna.toplevel.fa -m flip & ...
vcf snp written 23 days ago by goatsrunfaster10 • updated 23 days ago by RamRS22k
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Comment: C: Merge VCF files with diploid reference calls in different order for same positio
... Right, in one file the column REF has C T, while in the other REF reads T C for the same CHROM and POS. Note that I did not run this data through my own pipeline (although I wish I had). I am dealing with two VCF files that were created at two different times (using the same reference), and I want t ...
written 26 days ago by goatsrunfaster10
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Comment: C: Merge VCF files with diploid reference calls in different order for same positio
... No, they are the same, they are just in a different order. I one file C is before T, while in the other T is before C (yet the reference is diploid for C and T in either case). ...
written 26 days ago by goatsrunfaster10
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Merge VCF files with diploid reference calls in different order for same positions (e.g. TC vs CT)
... I'm trying to use VCF tools to merge two large VCF files for the same species. The problem I'm having is that the order of diploid calls for the reference is sometimes different between the two files (e.g. at pos 3445083 in 1 file the reference call is C T, whereas at pos 3445083 in the other VCF th ...
vcf snp written 26 days ago by goatsrunfaster10 • updated 26 days ago by finswimmer11k
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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 5 months ago by goatsrunfaster10
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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 3.1 years ago by goatsrunfaster10
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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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