Moderator: brentp

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brentp23k
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Salt Lake City, UT
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https://github.com/brentp
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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 14 months ago by brentp23k
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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 16 months ago by brentp23k
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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 16 months ago by brentp23k
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Comment: C: mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
... fixed. thanks. ...
written 16 months ago by brentp23k
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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 16 months ago by brentp23k • updated 16 months ago by ATpoint18k
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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 brentp23k
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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 brentp23k
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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 2.5 years ago by brentp23k
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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 2.6 years ago by brentp23k
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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 2.6 years ago by brentp23k

Latest awards to brentp

Teacher 13 months ago, created an answer with at least 3 up-votes. For A: What The Simplest/Easiest Open Source Genome Browser To Develop With? (For A Beg
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: How To Deal With Missing Genotypes In Population Pca Analysis
Teacher 13 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 13 months ago, created a question with more than 1,000 views. For Analyses With Case-Only Exomes
Epic Question 13 months ago, created a question with more than 10,000 views. For Good Gwas Papers / Resources
Good Answer 13 months ago, created an answer that was upvoted at least 5 times. For A: Bedtools Intersectbed
Good Answer 13 months ago, created an answer that was upvoted at least 5 times. For A: How To Separate Reads From Two Different Species In Exome Dataset?
Great Question 13 months ago, created a question with more than 5,000 views. For What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
Great Question 13 months ago, created a question with more than 5,000 views. For Good Gwas Papers / Resources
Appreciated 13 months ago, created a post with more than 5 votes. For A: How To Separate Reads From Two Different Species In Exome Dataset?
Appreciated 13 months ago, created a post with more than 5 votes. For C: Any Script To Parse Fasta Headers?
Scholar 14 months 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 14 months 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 14 months ago, created an answer with at least 3 up-votes. For A: Global Pairwise Alignment For Long Sequence Throws Error In Python!!
Commentator 15 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
Great Question 15 months ago, created a question with more than 5,000 views. For Good Gwas Papers / Resources
Teacher 19 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 20 months ago, created a question with more than 1,000 views. For vcfanno quickly annotate a vcf with other VCFs, BEDs, BAMs
Scholar 2.0 years ago, created an answer that has been accepted. For A: Using Rle (Relative Log Expression) Mean Values Of Microarray Data To Adjust For
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Global Pairwise Alignment For Long Sequence Throws Error In Python!!
Commentator 2.0 years 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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