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Moderator: brentp

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brentp ♦ 22k
Reputation:
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Location:
Salt Lake City, UT
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https://github.com/brentp
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brent_p
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Last seen:
1 week, 2 days ago
Joined:
7 years, 8 months ago
Email:
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Working on bionformatics at the Quinlan Lab at the University of Utah.

my code on github

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Posts by brentp

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Comment: C: Biallelic inactivation detection
... or use bcftools csq (https://academic.oup.com/bioinformatics/article/3000373/BCFtools/csq) which can annotate the effects using phase information. ...
written 4 months ago by brentp ♦ 22k
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Comment: C: Detection of CNVs from vcf file
... on the other hand, the benefit of the VCF over coverage-only methods is that you know the allele-balance. If the DP is high for a few variants and those same variants show an allele-balance (e.g. alt / ref+alt) of 0.66 or 0.33, then you can be fairly confident it's a CNV. ...
written 4 months ago by brentp ♦ 22k
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Answer: A: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 201
... Certainly the ExAC paper: http://www.nature.com/nature/journal/v536/n7616/full/nature19057.html must be one of the top. published in August and cited > 200 times already. It's a game-changer for rare disease. ...
written 9 months ago by brentp ♦ 22k
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Answer: A: How relevant, valuable, and important is Information Visualization nowadays in B
... If you can visualize data well, that means that you have the programming skills to parse and analyze the data. It means that you have enough of an understanding of the biology of the problem to know what visualizations and manipulations are useful. So, yes, there is a market for that. ...
written 11 months ago by brentp ♦ 22k
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Answer: A: Principal Component Analysis using SNP data ste
... If your data is in VCF format, you can do this with peddy: https://github.com/brentp/peddy The command would look like: python -m peddy -p 4 --plot --prefix my.out $vcf $ped this will do a PCA with your samples projected onto those from thousand genomes and ancestry predicted according to tho ...
written 11 months ago by brentp ♦ 22k
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Comment: C: Help with understanding CNVkit output
... so is it safe to assume that if the log2 < 0 it's a deletion, otherwise a dup? ...
written 15 months ago by brentp ♦ 22k
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Answer: A: What is the reason for most software errors in Bioinformatics according to you?
... The simple reason that software has bugs (that result in errors) is that **writing software is hard**. Let's take a simple example and say you want to write some software to determine if a genetic variant meets an **autosomal recessive inheritance pattern**. This is **easy**, right!? Just find sit ...
written 19 months ago by brentp ♦ 22k
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Comment: C: Black color reads in IGV: bwa-meth
... good to know ...
written 2.3 years ago by brentp ♦ 22k
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Tool: vcfanno quickly annotate a vcf with other VCFs, BEDs, BAMs
... We have been developing vcfanno for some time now as a tool to quickly and easily annotate (put stuff in the info field) of a VCF. It is very fast, and binaries are provided for all major systems for both 32 and 64bit. There is help in the README, for introduction, but here we'll briefly cover the ...
vcf annotation tool written 2.3 years ago by brentp ♦ 22k
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Comment: C: The new era of bioinformatics: simple and fast tools, fewer and more informative
... on the other hand, even small labs are doing dozens of whole genomes, requiring more infrastructure and analysts who are more than technicians.   ...
written 2.4 years ago by brentp ♦ 22k

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