Does anyone ever heard of anything that can convert bast output into sam or bam file? I'm doing all these analysis but I'm to lazy to figure out how to get the data from blast file that will match scores extracted from sam files
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There is a blast2sam.pl script in samtools. I never tested it. (misc directory) -
See also https://www.biostars.org/p/53434/ which has another suggestion: https://github.com/guyduche/Blast2Bam
As an aside, the NCBI seem to be working on native SAM output in BLAST+ itself:
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