Question: best way of filtering a VCF file using a list of SNP IDs and ref/alt alleles
0
gravatar for auraf85
3.0 years ago by
auraf8520
auraf8520 wrote:

Hi,

I need to filter a VCF file keeping only those SNPs that match with a separate list containing 3 columns: their ID, their reference allele and their alternate allele.

I am very new to this kind of procedure so I am trying to understand the most effective strategy to work on this.

I have been suggested to use VCFtools or BCFtools, but I am not sure I can select variants also on the basis of their ref/alt alleles. Is it possible to do this just using the command line?

Thank you

bcftools vcf • 1.9k views
ADD COMMENTlink modified 3.0 years ago by Pierre Lindenbaum123k • written 3.0 years ago by auraf8520
2
gravatar for harold.smith.tarheel
3.0 years ago by
United States
harold.smith.tarheel4.4k wrote:

If your separate list with IDs is formatted the same way as the VCF, then a simple grep should work:

grep -f ID.list full.vcf > filtered.vcf

Edit: Just realized that this command will remove the headers. Quickest solution is to add a line at the top of the ID.list that has the '#' character.

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by harold.smith.tarheel4.4k

hey, this works but it takes a very long time. What I did instead was adding reference and alternate allele letters to SNP id column and then use VCFtools to make selection.

ADD REPLYlink written 2.9 years ago by auraf8520
2
gravatar for Pierre Lindenbaum
3.0 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum123k wrote:

gatk https://software.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_variantutils_SelectVariants.php

Select IDs in fileKeep and exclude IDs in fileExclude:

 java -jar GenomeAnalysisTK.jar \
   -R ref.fasta \
   -T SelectVariants \
   --variant input.vcf \
   -o output.vcf \
   -IDs fileKeep \
   -excludeIDs fileExclude
ADD COMMENTlink written 3.0 years ago by Pierre Lindenbaum123k
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