User: kirannbishwa01

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Posts by kirannbishwa01

<prev • 240 results • page 1 of 24 • next >
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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 8 weeks ago by kirannbishwa01810
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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 9 weeks ago by kirannbishwa01810
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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 9 weeks ago by kirannbishwa01810 • updated 9 weeks ago by finswimmer3.6k
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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 9 weeks ago by kirannbishwa01810
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Comment: C: bcftools consensus not working when using -H flag
... @ finswimmer: I am still getting exactly the same error message. ...
written 9 weeks ago by kirannbishwa01810
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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 9 weeks ago by kirannbishwa01810
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Comment: C: bcftools consensus not working when using -H flag
... @fin swimmer: Did you had chance to look at this issue ? ...
written 9 weeks ago by kirannbishwa01810
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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 9 weeks ago by kirannbishwa01810
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bcftools consensus not working when using -H flag
... I am trying to get both the left and right reference genome using a sample name in phase VCF file. This works: bcftools consensus -f lyrata_chr01-short.fasta phasedVCF-short.vcf.gz -s ms01e -H 1 > ms01e-left.fa This doens't work though: when I am trying to make the new Ref Sequence ...
vcf software error bcftools reference genome written 9 weeks ago by kirannbishwa01810 • updated 8 weeks ago by finswimmer3.6k
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Answer: A: VCF file manipulation for extracting the required information
... For emperical biologist, I wrote this simple tool just for that purpose. https://www.biostars.org/p/309431/ https://github.com/everestial/VCF-simplify The only addition required is "zygosity" which I can add if need be. - Let me know. If you are a programmer than @finswimmer tools might give you ...
written 12 weeks ago by kirannbishwa01810

Latest awards to kirannbishwa01

Popular Question 29 days ago, created a question with more than 1,000 views. For Haplotype phasing for non-human model organism
Guru 3 months ago, received more than 100 upvotes.
Popular Question 3 months ago, created a question with more than 1,000 views. For error while using picard 2.1.0
Scholar 4 months ago, created an answer that has been accepted. For A: How to select aligned reads below certain mapping Quality (from BWA)?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Why GATK and bcftools SNP calling different?
Good Answer 4 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 4 months ago, created a question with more than 1,000 views. For How to add custom fields to the VCF files?
Appreciated 7 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 7 months ago, created a question with more than 1,000 views. For How to add custom fields to the VCF files?
Popular Question 8 months ago, created a question with more than 1,000 views. For How to add custom fields to the VCF files?
Popular Question 8 months ago, created a question with more than 1,000 views. For How to add custom fields to the VCF files?
Popular Question 9 months ago, created a question with more than 1,000 views. For error while using picard 2.1.0
Popular Question 10 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 10 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 11 months ago, created a question with more than 1,000 views. For How to remove kmer profiles?
Popular Question 13 months ago, created a question with more than 1,000 views. For How to remove kmer profiles?
Scholar 13 months ago, created an answer that has been accepted. For A: How to select aligned reads below certain mapping Quality (from BWA)?
Popular Question 14 months ago, created a question with more than 1,000 views. For How to remove kmer profiles?

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