User: kirannbishwa01

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kirannbishwa011.2k
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Posts by kirannbishwa01

<prev • 245 results • page 1 of 25 • next >
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Comment: C: Segmentation fault error while running extractPIRs from ShapeIT
... That was 3 years ago. Sorry to say, that I dont remember the context of the problem right now. Not sure, but If you are trying to extract readbackedphased haplotype and runs phasing VCF-SIMPLIFY https://github.com/everestial/VCF-Simplify and other tools in my repo could be helpful. Thanks, ...
written 14 months ago by kirannbishwa011.2k
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Comment: C: VCF-simplify: a VCF simplification tool.
... @qaedi This tool doesn't support this feature at the moment. As suggested by RamRS you may write a simple python or awk script. I however do have a plan to add that feature in a VCF parser I am currently building and also add that to VCF SIMPLIFY. It will be sometime before it rolls out though. ...
written 14 months ago by kirannbishwa011.2k
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Answer: A: VCF-simplify: a VCF simplification tool.
... VCFSIMPLIFY is updated with new features - https://github.com/everestial/VCF-Simplify/releases/tag/v3.0.1 , https://github.com/everestial/VCF-Simplify - External dependencies are removed, so only `python 3.6 or above` is enough. - Option to cythonize has been added to optimize run time. - M ...
written 14 months ago by kirannbishwa011.2k
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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 2.2 years ago by kirannbishwa011.2k
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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 2.3 years ago by kirannbishwa011.2k
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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 2.5 years ago by kirannbishwa011.2k
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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 2.5 years ago by kirannbishwa011.2k
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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 2.5 years ago by kirannbishwa011.2k • updated 2.5 years ago by finswimmer14k
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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 2.5 years ago by kirannbishwa011.2k
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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 2.5 years ago by kirannbishwa011.2k

Latest awards to kirannbishwa01

Popular Question 3 months ago, created a question with more than 1,000 views. For Using GEO datasets from NCBI for EHH (extended haplotype homozygosity) test
Appreciated 5 months ago, created a post with more than 5 votes. For A: Bedtools Genomecoveragebed Usage : How To Create A Genome File?
Popular Question 6 months ago, created a question with more than 1,000 views. For VCF isnot compressed and indexed even after running bgzip and tabix,
Popular Question 6 months ago, created a question with more than 1,000 views. For Using GEO datasets from NCBI for EHH (extended haplotype homozygosity) test
Popular Question 9 months ago, created a question with more than 1,000 views. For VCF isnot compressed and indexed even after running bgzip and tabix,
Popular Question 9 months ago, created a question with more than 1,000 views. For Calculate AB (allele balance) using SnpEff/SnpSift
Great Question 9 months ago, created a question with more than 5,000 views. For bcftools merge of multiple vcf produces duplicate records. How to solve the issue.
Popular Question 9 months ago, created a question with more than 1,000 views. For Using GEO datasets from NCBI for EHH (extended haplotype homozygosity) test
Popular Question 14 months ago, created a question with more than 1,000 views. For Calculate AB (allele balance) using SnpEff/SnpSift
Popular Question 14 months ago, created a question with more than 1,000 views. For VCF isnot compressed and indexed even after running bgzip and tabix,
Popular Question 14 months ago, created a question with more than 1,000 views. For Using GEO datasets from NCBI for EHH (extended haplotype homozygosity) test
Great Question 14 months ago, created a question with more than 5,000 views. For bcftools merge of multiple vcf produces duplicate records. How to solve the issue.
Popular Question 14 months ago, created a question with more than 1,000 views. For Genotype matrix to vcf snp database
Great Question 14 months ago, created a question with more than 5,000 views. For All the reads aligned using STAR have low mapping quality (0-3). What is happening?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Why GATK and bcftools SNP calling different?
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: How to plot coverage and depth statistics of a bam file
Popular Question 14 months ago, created a question with more than 1,000 views. For Handling/Extracting genome matrix file
Popular Question 14 months ago, created a question with more than 1,000 views. For error while using picard 2.1.0
Student 16 months ago, asked a question with at least 3 up-votes. For How to select aligned reads below certain mapping Quality (from BWA)?
Popular Question 16 months ago, created a question with more than 1,000 views. For VCF isnot compressed and indexed even after running bgzip and tabix,
Popular Question 17 months ago, created a question with more than 1,000 views. For Allele specific expression (ASE) using TPM (transcripts per million) values
Popular Question 20 months ago, created a question with more than 1,000 views. For VCF isnot compressed and indexed even after running bgzip and tabix,
Popular Question 20 months ago, created a question with more than 1,000 views. For Allele specific expression (ASE) using TPM (transcripts per million) values
Great Question 20 months ago, created a question with more than 5,000 views. For How to select aligned reads below certain mapping Quality (from BWA)?

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