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9.1 years ago
xinhui.wang
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550
I am running vcftools to get ped file from a list of vcf files. I would like to know the reference allele for these snps and I already download the fa file from http://www.ensembl.org/info/data/ftp/index.html
However, is there some tool with which I could extract the allele information for each SNP?
Thanks and with best regards,
Xinhui
Dear Pierre, Thanks. However, i had a huge list of SNP''s in my vcf file. do you mind to show me one command hoe to index the reference and search each positon and samtools faidx is a little diffcult for me. Thanks and with best regards, Xinhui
something like this:
Dear Pierre,
Thanks and it worked very well. However, the output is on screen and I would like to output results to a txt file. Could you help me a little more with that? Sorry I am not familiar with linux.
With best regards,
Xinhui