Moderator: brentp
brentp ♦ 22k
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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 8 days 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 28 days ago by
brentp ♦ 22k
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... 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 5 months ago by
brentp ♦ 22k
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... 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 7 months ago by
brentp ♦ 22k
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... 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 7 months ago by
brentp ♦ 22k
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... so is it safe to assume that if the log2 < 0 it's a deletion, otherwise a dup? ...
written 11 months ago by
brentp ♦ 22k
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... 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 15 months ago by
brentp ♦ 22k
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... 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 ...
written 24 months ago by
brentp ♦ 22k
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... on the other hand, even small labs are doing dozens of whole genomes, requiring more infrastructure and analysts who are more than technicians.
...
written 2.1 years ago by
brentp ♦ 22k
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