Moderator: brentp
brentp ♦ 23k
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Posts by brentp
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... Here is the current list of sites: https://github.com/brentp/peddy/blob/master/peddy/1kg.sites
There is a grad student in the lab working on allowing any set of sites (so we can support hg38 and any genome build). I hope this will be out soon, but I think he has some work yet to do. You can track t ...
written 14 months ago by
brentp ♦ 23k
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... that was the original design, but now it outputs to a file. that file is bgzipped and indexed on-the-fly so it gives similar utility to bigwig. ...
written 16 months ago by
brentp ♦ 23k
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... I see the utility of this, but I don't have any plans to do it. It would require wrapping Devon's libBigWig and then adding an additional option to output that instead of BED. I don't think this would make it too much faster--maybe a few percent if the user chose to output per-base depth. ...
written 16 months ago by
brentp ♦ 23k
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... mosdepth is a command-line tool for fast depth calculation. Because of the underlying algorithm it is possible to build a lot of features around the calculation. For example, once depth is calculated for every base in a chromosome, mosdepth can calculate the mean coverage in each of 100K intervals i ...
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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 2.0 years ago by
brentp ♦ 23k
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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 2.1 years ago by
brentp ♦ 23k
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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 2.5 years ago by
brentp ♦ 23k
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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 2.6 years ago by
brentp ♦ 23k
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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 2.6 years ago by
brentp ♦ 23k
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For vcfanno quickly annotate a vcf with other VCFs, BEDs, BAMs
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