Moderator: Zev.Kronenberg

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zevkronenberg
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Postdoc in the Eichler lab.  Studying structural variant and its role in disease and human evolution.

Posts by Zev.Kronenberg

<prev • 961 results • page 1 of 97 • next >
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Answer: A: Fast kmer reverse complement code using bit tricks
... This function is basically exactly the same as the OP, but it has a complement. In my testing the OP only reversed the bits. This is my encoding {0:A, 1:C, 2:G, 3:T} : uint64_t ReverseComp64(const uint64_t mer, uint8_t kmerSize) { uint64_t res = ~mer; res = ((res &g ...
written 9 months ago by Zev.Kronenberg11k
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Comment: C: Fast kmer reverse complement code using bit tricks
... This post is old, but it's worth mentioning that this function either has a bug, or based on my testing, is not complete. See my answer below. ...
written 9 months ago by Zev.Kronenberg11k
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Answer: A: vcflib-popstats to calculate FIS of a subpopulation
... Hi https://www.biostars.org/u/42177/, The genotype object, stored in var.cpp, contains the methods to calculate various statistics. I used the equation below to calculate FIS, where `nhet` is the count of the heterozygous genotypes, and `ngeno` is the number of called genotypes, `af`, is the allele ...
written 15 months ago by Zev.Kronenberg11k
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Answer: A: Keep only reads where both map using BBTools
... Hi Dylan, I wrote a tool, `Matlock`, for filtering read-pairs. It applies a set of filters to read-pairs rather than just on read at a time. It assumes the SAM/BAM/CRAM is read-pair sorted and no secondary or alternative alignments. https://github.com/phasegenomics/matlock ...
written 20 months ago by Zev.Kronenberg11k
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Answer: A: comparing two illumina genotypes report
... How about converting the files to VCF then using one of many VCF comparison tools? ...
written 3.2 years ago by Zev.Kronenberg11k
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Comment: C: tool to compare sv between two files
... It is simply a confidence interview around the start and end of the SV. By default I set it to ten. When multiple SVs are merged it gets wider. ...
written 3.3 years ago by Zev.Kronenberg11k
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Answer: A: tool to compare sv between two files
... One simple way to do this is to merge the SV calls and look at which calls collapse. I've writing some code to do this in VCF format. https://github.com/zeeev/mergeSVcallers ...
written 3.3 years ago by Zev.Kronenberg11k
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Comment: C: how to run STRUCTURE command n times for each K value?
... https://www.biostars.org/u/20/ No problem, see edited answer. I love how fast and sleazy perl is. ...
written 3.3 years ago by Zev.Kronenberg11k
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Answer: A: how to run STRUCTURE command n times for each K value?
... Since perl is still cool. Here's the gist, perl -e 'print join "\n", (0..10)' | xargs -I {} -P 10 admixture -K {} -o {}.something Edited: perl -e 'print join "\n", ((0..10) x 15)' | xargs -I {} -P 10 admixture -K {} -o {}.something ...
written 3.3 years ago by Zev.Kronenberg11k
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Comment: C: Multiple hypothesis testing, Fst outliers
... It really depends on the study. In the case of the Ephb2 (head crest), the allele was recessive so we were able to reach significance. If i remember correctly, pFst withstood a multiple test correction. ...
written 3.6 years ago by Zev.Kronenberg11k

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