Moderator: brentp

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brentp22k
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Salt Lake City, UT
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https://github.com/brentp
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4 weeks ago
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8 years, 3 months ago
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Working on bionformatics at the Quinlan Lab at the University of Utah.

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Posts by brentp

<prev • 945 results • page 1 of 95 • next >
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Answer: A: Obtaining list of / specifying interrogation sites in Peddy
... 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 7 weeks ago by brentp22k
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Comment: C: mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
... 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 4 months ago by brentp22k
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Comment: C: mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
... 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 4 months ago by brentp22k
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Comment: C: mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
... fixed. thanks. ...
written 4 months ago by brentp22k
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Tool: mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
... 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 ...
exome wgs depth coverage tool written 4 months ago by brentp22k • updated 4 months ago by ATpoint4.4k
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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 12 months ago by brentp22k
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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 13 months ago by brentp22k
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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 17 months ago by brentp22k
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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 19 months ago by brentp22k
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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 19 months ago by brentp22k

Latest awards to brentp

Scholar 7 weeks ago, created an answer that has been accepted. For A: Using Rle (Relative Log Expression) Mean Values Of Microarray Data To Adjust For
Good Answer 9 weeks ago, created an answer that was upvoted at least 5 times. For A: How To Separate Reads From Two Different Species In Exome Dataset?
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Global Pairwise Alignment For Long Sequence Throws Error In Python!!
Commentator 11 weeks ago, created a comment with at least 3 up-votes. For C: How To Find Out Whether There Is A Statistical Difference Between Two Sets Of St
Great Question 11 weeks ago, created a question with more than 5,000 views. For Good Gwas Papers / Resources
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Global Pairwise Alignment For Long Sequence Throws Error In Python!!
Popular Question 8 months ago, created a question with more than 1,000 views. For vcfanno quickly annotate a vcf with other VCFs, BEDs, BAMs
Scholar 12 months ago, created an answer that has been accepted. For A: Using Rle (Relative Log Expression) Mean Values Of Microarray Data To Adjust For
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Global Pairwise Alignment For Long Sequence Throws Error In Python!!
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: How To Find Out Whether There Is A Statistical Difference Between Two Sets Of St
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Popular Question 15 months ago, created a question with more than 1,000 views. For Batmeth: Improved Mapper For Bisulfite Sequencing Reads On Dna Methylation
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Scholar 17 months ago, created an answer that has been accepted. For A: Using Rle (Relative Log Expression) Mean Values Of Microarray Data To Adjust For
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Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Global Pairwise Alignment For Long Sequence Throws Error In Python!!

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