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
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
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.
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
bcftools view will do this quickly and easily.
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