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
    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'

