User: kirannbishwa01

gravatar for kirannbishwa01
Reputation:
860
Status:
Trusted
Location:
United States
Last seen:
4 days, 13 hours ago
Joined:
3 years, 7 months ago
Email:
k*************@gmail.com

Posts by kirannbishwa01

<prev • 242 results • page 1 of 25 • next >
1
vote
3
answers
2.4k
views
3
answers
Comment: C: How to add custom fields to the VCF files?
... It is surprising that you don't have `SAMPLE` and `FORMAT`. I suggest using awk to move the data around or extract the data out of your `INFO` column. If you are familiar with python that should make it even easier. If you are fairly new to bioinformatics and not familiar with building your own scr ...
written 15 days ago by kirannbishwa01860
0
votes
0
answers
121
views
0
answers
Benchmarking datasets for Haplotype phasing
... I have been trying to run a benchmark test on one the haplotype phasing application. I tried to navigate around to find tutorials for it and found this to be a good one: https://portal.biohpc.swmed.edu/content/training/bioinformatics-nanocourses/gwas/zhan-phasing-workshop/ I like this tutorial bec ...
genome shapeit haplotype na12891 phasing written 4 weeks ago by kirannbishwa01860
0
votes
0
answers
182
views
0
answers
GFF liftOver using CrossMap is failing.
... I am trying to lift over a GFF, GTF using the Chain file generated from VCF. I am using `CrossMap` as well as `liftOver` from UCSC. LiftOver isn't working. CrossMap is giving me an output but it indicates that there are failures. Upon looking at those position in the `Chain` and `original GFF` fil ...
software error gff crossmap liftover written 4 months ago by kirannbishwa01860
0
votes
1
answer
326
views
1
answers
Comment: C: bcftools consensus not working when using -H flag
... I will try that tomorrow. I tried to take a different approach to this problem, but another issue came up. I raised a github issue. If you can shed light on the problem. Thanks for beginning helpful ! ...
written 4 months ago by kirannbishwa01860
0
votes
1
answer
193
views
1
answer
Coverting missing sites to reference allele using Bcftools isn't working.
... I am trying to set the missing `GT = . to 0|0` but while using `bcftools` I end up only with `GT as single 0` in all the missing sites for all the samples. **Initial VCFs:** CHROM POS ID REF ALT QUAL FILTER INFO FORMAT MA605 MA611 MA622 MA625 MA629 Ncm8 Sp154 Sp164 Sp21 Sp3 Sp76 SpNor33 ms0 ...
vcf software error bcftools genotype genome written 4 months ago by kirannbishwa01860 • updated 4 months ago by finswimmer5.4k
0
votes
1
answer
326
views
1
answers
Comment: C: bcftools consensus not working when using -H flag
... @fin swimmer: I have been trying to fix this issue by playing with `-i and -e ` using the manual. But, still cannot find the fix. ...
written 4 months ago by kirannbishwa01860
0
votes
1
answer
326
views
1
answers
Comment: C: bcftools consensus not working when using -H flag
... @ finswimmer: I am still getting exactly the same error message. ...
written 4 months ago by kirannbishwa01860
0
votes
1
answer
326
views
1
answers
Comment: C: bcftools consensus not working when using -H flag
... @cpad : that is already tested and works. But, I don't want to add a dummy GT in there - which on large data is lots of work. Since, I am trying to create a personal genome here, an empty `GT = "."` for any sample of interest should be automatically treated as reference allele. I believe this is j ...
written 4 months ago by kirannbishwa01860
0
votes
1
answer
326
views
1
answers
Comment: C: bcftools consensus not working when using -H flag
... @fin swimmer: Did you had chance to look at this issue ? ...
written 4 months ago by kirannbishwa01860
0
votes
1
answer
326
views
1
answers
Comment: C: bcftools consensus not working when using -H flag
... @finswimmer: Here is my VCF data: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT MA605 MA611 MA622 MA625 MA629 Ncm8 Sp154 Sp164 Sp21 Sp3 Sp76 SpNor33 ms01e ms02g ms03g ms04h 1 141 . C T . . . GT:PG:PG_al:PI . . . 0|1:0|1:C|T:10763 . . . . . . . . . . . . 1 3697 . T C . . . GT:PG:PG_al:P ...
written 4 months ago by kirannbishwa01860

Latest awards to kirannbishwa01

Popular Question 3 months ago, created a question with more than 1,000 views. For Haplotype phasing for non-human model organism
Guru 5 months ago, received more than 100 upvotes.
Popular Question 5 months ago, created a question with more than 1,000 views. For error while using picard 2.1.0
Scholar 6 months ago, created an answer that has been accepted. For A: How to select aligned reads below certain mapping Quality (from BWA)?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Why GATK and bcftools SNP calling different?
Good Answer 6 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
Popular Question 6 months ago, created a question with more than 1,000 views. For How to add custom fields to the VCF files?
Appreciated 9 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 9 months ago, created a question with more than 1,000 views. For How to add custom fields to the VCF files?
Popular Question 10 months ago, created a question with more than 1,000 views. For How to add custom fields to the VCF files?
Popular Question 10 months ago, created a question with more than 1,000 views. For How to add custom fields to the VCF files?
Popular Question 11 months ago, created a question with more than 1,000 views. For error while using picard 2.1.0
Popular Question 12 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 12 months ago, created a question with more than 1,000 views. For How to select aligned reads below certain mapping Quality (from BWA)?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 709 users visited in the last hour