Question: Converting blastn output to VCF (for SNPs): what is the quickest way?
gravatar for Macspider
19 months ago by
Vienna - BOKU
Macspider3.0k wrote:

Hello guys,

Title is pretty self-explanatory: what is the quickest way to convert the output of command line blast (say xml format, but I'm open to any suggestion) to a pseudo-VCF file?

I am interested in getting all the positions where I have a SNP (mismatch) between query and subject. Doesn't have to be a VCF or pseudo-VCF by force, I just need scaffold + position + variant.

I guess this question has been asked a lot, but I can't seem to find any answer. Would you suggest me something / link me something that I might have missed?

convert snp blast xml vcf • 699 views
ADD COMMENTlink written 19 months ago by Macspider3.0k

duplicate/see Find Mismatch And Gap Positions

ADD REPLYlink written 19 months ago by Pierre Lindenbaum124k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1945 users visited in the last hour