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Questions - vcf-variant-call-format

Issue with map file output from plink

I am working with the vcf file (generated using bcftools) to create a map file using plink software. The command i am using is ./plink --vcf sample.vcf --out sample --recode --allow-extra-chr The ou...
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Tania

genetics

vcf-variant-call-format

map-files

Votes: 0

Answers: 1

Latest Answer

The third column of the map file represents the position of the variants based on the recombination map: https://www.cog-genomics.org/plink/1.9/formats#map This field is optional and I assume your inp...
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Yosuke Tanigawa

select uniquely mapped genes to SNP

I have a vcf and want to select 100 genes, and for each gene, to select one SNP? Technically if we consider one gene it has many rsid mapped to it. For my analysis I need to select 100 genes and for e...
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Rhea Bedi

r

filter

code-generation

genome

vcf-variant-call-format

Votes: 0

Answers: 1

Latest Answer

Consider str.split of the pipe-delimited column in ANN for the gene which is about the fourth pipe. Then run a sequential count by the gene grouping with ave. Then subset group number for the 1. Pleas...
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Parfait

NGS Analysis: How can I extract the different variants in two VCF files

I am currently working on my thesis and I am trying to analyze the results of NGS sequencing Illumina. I am not really familiar with bioinformatics and in this part of my project, I am trying two comp...
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eleni.ps

compare

bioinformatics

data-analysis

data-annotations

vcf-variant-call-format

Votes: 0

Answers: 1

Latest Answer

I understand your problem. First thing I would recommend is to use Unix software (I don't know which OS you're running) called VCFtools. It's pretty simple to use. But if You want to do all the proce...
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777moneymaker

How to run ensembl-vep in conda

I’ve installed like so: conda install ensembl-vep=105.0-0 And then installed the human cache like this: vep_install -a cf -s homo_sapiens -y GRCh38 -c /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdf...
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Mike

variant

vcf-variant-call-format

vcftools

gatk

Votes: 0

Answers: 1

Latest Answer

I found the answer. You need to add both --cache and --dir_cache arguments: vep --cache --dir_cache "/mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/conda/envs/bioinfo/share/ensembl-vep-105....
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Mike

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