difficulty filtering vcf file with vcftools

Question

[Phoebe Magdy]

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

[4galaxy77]

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 vcftools is very outdated now and is not under maintaience.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?

[Phoebe Magdy]

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

Answer 1

[4galaxy77]

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

[Phoebe Magdy]

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"