how do you download a single SNP in vcf format?
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5.4 years ago
doirerosie • 0

how do you download a single SNP in vcf format? I want to load in into a variant effect predictor tool and it must be in vcf Doire

SNP • 868 views
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5.4 years ago
Ram 44k

VEP does not need every column of the VCF format, only chr, pos, ref and alt. Those values should be straightforward to extract from a SNP entry.

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5.4 years ago
Ace ▴ 90

you could filter it with vcftools

vcftools --vcf $vcf --positions SNP_list.txt --recode --out $out

or

vcftools --vcf $vcf --chr $chr --from-bp $start --to-bp $end --recode --out $out

The advantage of that is that it will also work with gzvcf or for multiple SNPs, but honestly, it's probably just as easy to extract using cat | grep in a vcf as mentioned above

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5.4 years ago
Brice Sarver ★ 3.8k

bcftools view will do this quickly and easily.

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