Question: Converting blastn output to VCF (for SNPs): what is the quickest way?
0
gravatar for Macspider
19 months ago by
Macspider3.0k
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
1

duplicate/see Find Mismatch And Gap Positions

ADD REPLYlink written 19 months ago by Pierre Lindenbaum124k
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