Moderator: Zev.Kronenberg

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https://eichlerlab.gs....
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zevkronenberg
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Joined:
7 years, 8 months ago
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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 • 959 results • page 1 of 96 • next >
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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 3 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 23 months 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 23 months 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 24 months 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 24 months 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 24 months 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 2.3 years ago by Zev.Kronenberg11k
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Answer: A: metagenomic profiling and population analysis
... Here's a paper out of my old lab: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0969-1 ...
written 2.3 years ago by Zev.Kronenberg11k
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building all possible phylogenies.
... Given a starting phylogeny, something like: (susie_ggo,(clint_ptr,(yri_hsa,chm13_hsa)),susie_pab); Is there a tool to generate all other possible trees? i.e: (susie_ggo,(clint_ptr,(yri_hsa,chm13_hsa)),susie_pab); (clint_ptr,(susie_ggo,(yri_hsa,chm13_hsa)),susie_pab); (susie_ggo,( ...
phylogenetics written 2.3 years ago by Zev.Kronenberg11k • updated 2.3 years ago by h.mon26k
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Answer: A: Multiple hypothesis testing, Fst outliers
... Chris, I'm happy to hear people are using GPAT code within VCFLIB. While unpublished, there is a working manuscript in the VCF github. I've tried to describe, in better detail, what pFst and other GPAT tools do. pFst is terribly named (i don't take responsibility), because it is a likelihood ra ...
written 2.3 years ago by Zev.Kronenberg11k

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