Question: How to obtain SNP positions for specific mouse strain using VCF from Sanger Institute ftp server?
1
gravatar for Ankit
11 months ago by
Ankit130
Ankit130 wrote:

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 jf1 strain mouse vcf • 439 views
ADD COMMENTlink modified 11 months ago by Pierre Lindenbaum126k • written 11 months ago by Ankit130
3
gravatar for Pierre Lindenbaum
11 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum126k wrote:
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'
ADD COMMENTlink written 11 months ago by Pierre Lindenbaum126k

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

ADD REPLYlink modified 11 months ago • written 11 months ago by Ankit130
1

check you're using the latest version of bcftools

ADD REPLYlink written 11 months ago by Pierre Lindenbaum126k
1

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

ADD REPLYlink written 11 months ago by Ankit130
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