Compare results from different aligners (SAM files)

[guykol]

I would like to take 2 SAM files that are the results of alignment of the same input by different aligners and compare them.
Does anyone know of a code that already does that?

Thanks,

Guy.

[epigen]

I already asked that and noone could provide me with any useful code, see

http://seqanswers.com/forums/showthread.php?t=5666

So I hope someone might give a positive answer here.

[Dethecor]

Define "Compare"

Maybe if you could specify what you want to compare there would be a bigger chance that someone will provide more useful information.

To me it sounds like something you would do on your own with a little script in whatever programming language you like best
You could for example use samtools to sort both files and then use awk or whatever you like to check which reads are aligned in the same spot and which are not o.O

[Bruins]

I'm interested too.

I will be looking at this sometime in the near future (before August), I'll post whatever methods I use/come up with then.

[mistro]

I came across this utility

http://genome.sph.umich.edu/wiki/BamUtil:_diff

$bam diff --in1 file1.sam/bam --in2 file2.sam/bam --out file1.fil2.diff.sam/bam

This will create three sam or bam files. proceeding from there...