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Questions - vcftools

Extract variant positions from VCF dependent on contents of other columns

I have a vcf file, I am trying to extract the information from these columns: #CHROM POS REF ALT However I would like to extract these only if the SAMPLE-1 column contains the string DeNovo (N...
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hdjc90

awk

sed

samtools

vcftools

bcftools

Votes: 0

Answers: 1

Latest Answer

FWIW, I'm not familiar with bcftools but if the intention is to pipe the bcftools output into awk then we could do the whole thing in awk ... Assumptions: none of the fields (in the file) contain whi...
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markp-fuso

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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