extracting SNPs from .vcf file along with CHR and POS

Question

[anamaria]

Hello,

I download file 00-All.vcf.gz from https://ftp.ncbi.nih.gov/snp/pre_build152/organisms/human_9606_b150_GRCh37p13/VCF/

I need to extract a list of SNPs (which I put in META_rs) from there long with their CHR# and position I am doing this:

vcftools --gzvcf 00-All.vcf.gz --snps META_rs --recode --out  META_RSID

Is this correct way to go about this? the command takes a long time to execute...

Thanks Ana

[Kevin Blighe]

Seems that you got the answer here!

Answer 1

[Ram]

vcftools is obsolete, I think. Use bcftools instead. You should be able to use

bcftools query -Hf '%CHROM\t%POS\t%REF\t%ALT\t%ID\n' 00-Al.vcf.gz

Customize the format string to get what you exactly need.

EDIT (29-Nov-2021)

I might be wrong about vcftools being obsolete. There is also a catch with extracting loci from VCF files - the VCF may not be left-aligned, and it might have multi-allelic entries, which would interfere with operations that rely on matching CHR-POS-REF-ALT entries. One should use either vt (vt decomp, then vt normalize) or bcftools norm -m to pre-process the VCF before extracting fields, as POS, REF and ALT for certain entries might change after these operations. vt is better than bcftools IMO as it retains the old multi-allelic/pre-left-aligned information as INFO entries.