extracting SNPs from .vcf file along with CHR and POS
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10 months ago
anamaria ▴ 160

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

vcftools • 418 views
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Seems that you got the answer here!

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10 months ago
Ram 32k

vcftools is obsolete, I think.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.

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