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  • Compare results from different aligners (SAM files)

    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.

  • #2
    I already asked that and noone could provide me with any useful code, see
    Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc

    So I hope someone might give a positive answer here.

    Comment


    • #3
      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

      "You are only young once, but you can stay immature indefinitely."

      Comment


      • #4
        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.

        Comment


        • #5
          I came across this utility


          $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...

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