User: kirannbishwa01

gravatar for kirannbishwa01
Reputation:
770
Status:
Trusted
Location:
United States
Last seen:
15 hours ago
Joined:
3 years, 2 months ago
Email:
k*************@gmail.com

Posts by kirannbishwa01

<prev • 230 results • page 1 of 23 • next >
0
votes
0
answers
127
views
0
answers
Comment: C: VCF-simplify: a VCF simplification tool.
... I had sometime to think over your question. Symbolic variants can only be mined if `cyvcf2` has a method built into it - which I think there is none. Because, symbolic allele would need a method to interpret that symbol (be it a deletion overlapping variant, inversion etc.). Symbolic variants only m ...
written 4 days ago by kirannbishwa01770
1
vote
0
answers
127
views
0
answers
Comment: C: VCF-simplify: a VCF simplification tool.
... @Kevin : Looks like a good add on methods to the tool. The implementation shouldn't take long. I will have to think if there is already a GATK method to do so for "A" and add it to the `INFO` field, so I am not reinventing the wheel. "B" looks like an extensive version of "B". Thanks, ...
written 4 days ago by kirannbishwa01770
0
votes
0
answers
127
views
0
answers
Comment: C: VCF-simplify: a VCF simplification tool.
... I haven't dealt with that directly. My assumption is it should report as it is. This tool is meant to simplify the VCF output in most possible simple way. So, the simplification is only limited to the structure of the output. It doesn't interpret field,tags. Specific Interpreted extraction of tag ...
written 5 days ago by kirannbishwa01770
4
votes
0
answers
127
views
5 follow
0
answers
Tool: VCF-simplify: a VCF simplification tool.
... # VCF-simplify.v2 A python parser to simplify the vcf file into table like format. https://github.com/everestial/VCF-simplify There are several tools available to mainpulate and alter VCF file. But, a simple and comprehensive tool that can produce a most simple output required by emperical biolog ...
vcf genome tool variants written 5 days ago by kirannbishwa01770
1
vote
1
answer
202
views
1
answers
Comment: C: bcftools merge of multiple vcf produces duplicate records. How to solve the issu
... My vcf's are merged and validated before piping into "phaser". The issue is "phaser" exclusively outputs single sample VCFs, which needs remerging - and when I try to merge I run into problems. I have not been able to find a tools that can fix the VCF format issue (but has correct information). Let' ...
written 6 weeks ago by kirannbishwa01770
0
votes
1
answer
202
views
1
answers
Comment: C: bcftools merge of multiple vcf produces duplicate records. How to solve the issu
... I have to add that it's not "PL" tag and values but "pi" tags and values. I think the character differences caused the issue. ...
written 6 weeks ago by kirannbishwa01770
0
votes
1
answer
202
views
1
answers
Comment: C: bcftools merge of multiple vcf produces duplicate records. How to solve the issu
... Yeah, GATK doesn't seem to be working well when data are piped in, if it came out of the GATK workflow. I have been in touch with Stephane Castel over the issue several times. But, it seems he is busy and not able to look over the problem. Or, prolly he has moved on. I know a little bit of pytho ...
written 6 weeks ago by kirannbishwa01770
0
votes
1
answer
202
views
1
answers
Comment: C: bcftools merge of multiple vcf produces duplicate records. How to solve the issu
... Kevin, This merging has been a big pain for me. GATK `CombineVariants` is throwing an error which I can't fix. And, `bcftools` now seem to be giving up too. I think I will need to the author of "phaser" to look into this problem. Thanks, ...
written 6 weeks ago by kirannbishwa01770
0
votes
1
answer
202
views
1
answers
Comment: C: bcftools merge of multiple vcf produces duplicate records. How to solve the issu
... I think the reason the "PI" are missing is because all the samples at that record don't have meaningful "PI" value. But, regardless of that shouldn't it be possible to have it in "merged VCFs". ...
written 6 weeks ago by kirannbishwa01770
1
vote
0
answers
100
views
0
answers
Comment: C: What is the structure of the data in Haplotype reference panel?
... Thank you Kevin. I asked it out of curiosity as of now; but will be working on "haplotype phasing" project of my own soon. Yes, that picture helps. Thanks a lot. ...
written 6 weeks ago by kirannbishwa01770

Latest awards to kirannbishwa01

Guru 4 days ago, received more than 100 upvotes.
Popular Question 20 days ago, created a question with more than 1,000 views. For error while using picard 2.1.0
Scholar 4 weeks ago, created an answer that has been accepted. For A: How to select aligned reads below certain mapping Quality (from BWA)?
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Why GATK and bcftools SNP calling different?
Good Answer 6 weeks ago, created an answer that was upvoted at least 5 times. For A: How to plot coverage and depth statistics of a bam file
Popular Question 7 weeks ago, created a question with more than 1,000 views. For How to add custom fields to the VCF files?
Appreciated 4 months ago, created a post with more than 5 votes. For A: How to plot coverage and depth statistics of a bam file
Popular Question 4 months ago, created a question with more than 1,000 views. For How to add custom fields to the VCF files?
Popular Question 5 months ago, created a question with more than 1,000 views. For How to add custom fields to the VCF files?
Popular Question 5 months ago, created a question with more than 1,000 views. For How to add custom fields to the VCF files?
Popular Question 6 months ago, created a question with more than 1,000 views. For error while using picard 2.1.0
Popular Question 7 months ago, created a question with more than 1,000 views. For How to select aligned reads below certain mapping Quality (from BWA)?
Popular Question 7 months ago, created a question with more than 1,000 views. For How to select aligned reads below certain mapping Quality (from BWA)?
Popular Question 8 months ago, created a question with more than 1,000 views. For How to remove kmer profiles?
Popular Question 10 months ago, created a question with more than 1,000 views. For How to remove kmer profiles?
Scholar 10 months ago, created an answer that has been accepted. For A: How to select aligned reads below certain mapping Quality (from BWA)?
Popular Question 11 months ago, created a question with more than 1,000 views. For How to remove kmer profiles?
Popular Question 11 months ago, created a question with more than 1,000 views. For Changing @RG header information in *.bam files using picard
Scholar 12 months ago, created an answer that has been accepted. For A: How to select aligned reads below certain mapping Quality (from BWA)?
Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: How to plot coverage and depth statistics of a bam file
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Bedtools Genomecoveragebed Usage : How To Create A Genome File?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 667 users visited in the last hour