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difficulty filtering vcf file with vcftools

I had a large VCF file named "common_known_variants.vcf " which contains all known human variants downloaded from https://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/VCF/00-common_all.vcf.gz as common_known_variants.vcf.gz

I'm trying to extract the known variants from only chromosomes 1,2,3,9,22, and X and write them in a new vcf file with the name targeted_known_variants.vcf so I created a txt file named targeted_chromosomes.txt each line had a no of chromosome from those I needed to extract and I used this command line in a jupyter notebook

!vcftools --vcf common_known_variants.vcf --positions targeted_chromosomes.txt --recode --recode-INFO-all --out targeted_known_variant

Unfortunately it created a new vcf file containing the headers only it seems that the command cannot read the txt file ,,, any help with this? I would be grateful

vcf vcftools
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updated by Ram Ram • written by Phoebe Magdy • Phoebe Magdy

Welcome Phoebe. vcftools is very outdated now and is not under maintaience. Please use bcftools instead. Am I right in thinking you just want to subset common_known_variants.vcf to contain only chromosomes 1,2,3,9,22, and X?

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written by 4galaxy77 4galaxy77

Am I right in thinking you just want to subset common_known_variants.vcf to contain only chromosomes 1,2,3,9,22, and X?

yes that is exactly what I want to do

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updated by Istvan Albert Istvan Albert • written by Phoebe Magdy • Phoebe Magdy

1 answer 

bcftools view \
    --regions 1,2,3,9,22,X \
    -O z \
    common_known_variants.vcf > targeted_known_variants.vcf

Note

  1. You will need to index the file first using bcftools index
  2. Check the naming of the chromosomes; i.e. whether they are chr1 or 1
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written by 4galaxy77 4galaxy77

Many thanks for your response [4galaxy77][1] it worked with me and I extracted a subset of the "common_known_variants.vcf.gz" file to contain only chromosomes 1,2,3,9,22, and X in another file named "targeted_known_variants.vcf.gz"

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written by Phoebe Magdy • Phoebe Magdy

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