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How to obtain SNP positions for specific mouse strain using VCF from Sanger Institute ftp server?

Hi everyone, I would like to get SNP positions of a particular strain of mouse (JF1) from VCF file deposited in ftp server of Sanger Institute. The link of the file is as follows: ftp://ftp-mouse.sanger.ac.uk/REL-1807-SNPs_Indels/mgp.v6.merged.norm.snp.indels.sfiltered.vcf.gz. It would be very helpful if somebody can suggest me a tool or way to do this. Thanks Ankit

snp vcf mouse jf1 strain
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by Ankit Ankit

1 answer 

wget -q -O - "ftp://ftp-mouse.sanger.ac.uk/REL-1807-SNPs_Indels/mgp.v6.merged.norm.snp.indels.sfiltered.vcf.gz" |\
bcftools view --samples "JF1_MsJ" |\
bcftools query -i 'INFO/AC>0'  -f '%CHROM  %POS\n'
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written by Pierre Lindenbaum Pierre Lindenbaum

check you're using the latest version of bcftools

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written by Pierre Lindenbaum Pierre Lindenbaum

Hi Pierre. I updated bcftools version. Command worked with that. Thanks

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written by Ankit Ankit

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