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Old 02-23-2010, 06:17 AM   #1
Location: wisconsin

Join Date: Jan 2010
Posts: 12
Default BLAT or BLAST: output SNPs between reference and query?

When using either BLAT or BLAST, does anyone know of a tool or script that takes the output from the alignment and calculates the positions of difference between the reference and query?

For example, BOWTIE returns something like this for each result: 64:G>N,66:G>N

It is possible to write perl or something to parse the output of BLAST or BLAT, but I'd rather not reinvent this if it's been done before.

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