Converting Blast Output To Sam Format

Question

[Wen.Huang]

Hi everybody,

I was wondering if there is a blast output parser that convert blast output to SAM format. There are many blast parser out there, but most for compressing results to more readable statistics. I would appreciate if anybody can point me to something that extracts the alignments.

Thanks!

[Peter]

The NCBI seem to be working on adding SAM output to BLAST+ directly, see http://blastedbio.blogspot.co.uk/2015/07/ncbi-working-on-sam-output-from-blast.html

[Rm]

http://www.biostars.org/post/show/13449/

Answer 1

[Istvan Albert]

The samtools source distribution contains a file called misc/blast2sam.pl that can convert the output of earlier versions of blast (use a blast release from around 2007). In the meantime the blast output has changed in subtle (and undocumented) ways, Heng Li has stated that this blast converter is not being maintained to operate for current versions of blast.

Answer 2

[Pierre Lindenbaum]

(2.8 years later:) I asked my student to write a blastn to sam converter. His C code is available at : https://github.com/guyduche/Blast2Bam

[Istvan Albert]

awesome! there are so many BAM file visualizers out there and none (that I know of ) for BLAST output