Question

Converting Blast Output To Sam Format

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12.3 years ago

Wen.Huang ★ 1.2k

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!

blast sam parser • 13k views

ADD COMMENT • link updated 9.5 years ago by Pierre Lindenbaum 164k • written 12.3 years ago by Wen.Huang ★ 1.2k

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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

ADD REPLY • link 9.3 years ago by Peter 6.0k

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

ADD REPLY • link 12.2 years ago by Rm 8.3k

score 7 · Answer 1 · 2012-09-22

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.

score 7 · Answer 2 · 2015-06-29

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9.5 years ago

Pierre Lindenbaum 164k

(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

ADD COMMENT • link 9.5 years ago by Pierre Lindenbaum 164k

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

ADD REPLY • link 9.5 years ago by Istvan Albert 102k