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

Question

[Ankit]

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

Answer 1

[Pierre Lindenbaum]

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'

[Ankit]

Hi Pierre, Thanks for the reply. I tried the command but it is giving error:

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'

view: invalid option -- '-' [main] Unrecognized command. open: No such file or directory

Please help with this. What I am doing wrong? Thanks

[Pierre Lindenbaum]

check you're using the latest version of bcftools

[Ankit]

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