Moderator: brentp
brentp ♦ 23k
- Reputation:
- 22,980
- Status:
- Trusted
- Location:
- Salt Lake City, UT
- Website:
- https://github.com/brentp
- Twitter:
- brent_p
- Scholar ID:
- Google Scholar Page
- Last seen:
- 6 months, 2 weeks ago
- Joined:
- 10 years, 1 month ago
- Email:
- b*******@gmail.com
Posts by brentp
<prev
• 946 results •
page 1 of 95 •
next >
1
vote
0
answers
3.4k
views
0
answers
... I updated the post to link to the new cadd docs. ...
written 6 months ago by
brentp ♦ 23k
2
votes
1
answer
552
views
1
answers
... 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 23 months ago by
brentp ♦ 23k
0
votes
1
answer
1.8k
views
1
answers
... 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 2.2 years ago by
brentp ♦ 23k
0
votes
1
answer
1.8k
views
1
answers
... 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 2.2 years ago by
brentp ♦ 23k
7
votes
1
answer
1.8k
views
1
answer
... 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 ...
3
votes
1
answer
833
views
1
answers
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 2.8 years ago by
brentp ♦ 23k
0
votes
3
answers
1.5k
views
3
answers
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 2.9 years ago by
brentp ♦ 23k
10
votes
2
answers
4.0k
views
2
answers
... 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 3.2 years ago by
brentp ♦ 23k
1
vote
4
answers
1.1k
views
4
answers
... 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 3.4 years ago by
brentp ♦ 23k
Latest awards to brentp
Teacher
10 months ago,
created an answer with at least 3 up-votes.
For A: Global Pairwise Alignment For Long Sequence Throws Error In Python!!
Scholar
10 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
10 months ago,
created an answer that was upvoted at least 5 times.
For A: Bedtools Intersectbed
Good Answer
10 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
10 months ago,
created a question with more than 5,000 views.
For Good Gwas Papers / Resources
Appreciated
10 months ago,
created a post with more than 5 votes.
For C: Any Script To Parse Fasta Headers?
Appreciated
10 months ago,
created a post with more than 5 votes.
For C: How To Find Out Whether There Is A Statistical Difference Between Two Sets Of St
Teacher
22 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
22 months ago,
created an answer with at least 3 up-votes.
For A: How To Deal With Missing Genotypes In Population Pca Analysis
Teacher
22 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
22 months ago,
created a question with more than 1,000 views.
For Analyses With Case-Only Exomes
Epic Question
22 months ago,
created a question with more than 10,000 views.
For Good Gwas Papers / Resources
Good Answer
22 months ago,
created an answer that was upvoted at least 5 times.
For A: Bedtools Intersectbed
Good Answer
22 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
22 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
22 months ago,
created a question with more than 5,000 views.
For Good Gwas Papers / Resources
Appreciated
22 months ago,
created a post with more than 5 votes.
For A: How To Separate Reads From Two Different Species In Exome Dataset?
Appreciated
22 months ago,
created a post with more than 5 votes.
For A: What The Simplest/Easiest Open Source Genome Browser To Develop With? (For A Beg
Appreciated
22 months ago,
created a post with more than 5 votes.
For C: Any Script To Parse Fasta Headers?
Appreciated
22 months ago,
created a post with more than 5 votes.
For C: How To Find Out Whether There Is A Statistical Difference Between Two Sets Of St
Scholar
23 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
23 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
23 months 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
Great Question
2.0 years ago,
created a question with more than 5,000 views.
For Good Gwas Papers / Resources
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1087 users visited in the last hour