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  • the "chr" in the chromosome name

    Hi,
    I have been given a few exome datasets (already mapped and I don't have the fastq files). The problem is that when these were mapped, they used a reference annotation that did not have the "chr" in with the chromosome ID. All of my other exomes that I have do have this annotation. As you can image, this is being a little problamatic when I am trying to do the analysis with all of the samples at the same time. Is there a simple way to add the "chr" to these samples without having to do all of the remapping?
    Thanks

  • #2
    You can use samtools reheader. Just samtools view -H file.bam > header.sam, then edit that to include the "chr" (don't change the ordering, though!). You can then use that for the reheader command. This assumes, of course, that this is the only difference between the genomes.

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    • #3
      Thanks,
      I thought that samtools reheader only changes the actual header info, but what about in all of the individual alignments? I do know that the same genome build was used for everything so that shouldn't be too much of a problem.

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      • #4
        In a BAM file, the actual chromosome name is only stored in the header (each read has an associated index number that is used by samtools or other programs to get the actual name of the chromosome/contig).

        If you have a SAM file then this won't work, you'll have to write a little script in python/perl/whatever.

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        • #5
          That makes sense. I never realized it worked that way.
          Thanks

          Comment


          • #6
            chromosome extraction without sorting

            I need suggestion to extract the chromosome or chromosome region (e.g. chr1: 100,000,000-200,000,000) without sorting bam file. Any idea related with this would be appreciated.

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            • #7
              Originally posted by bioinfo816 View Post
              I need suggestion to extract the chromosome or chromosome region (e.g. chr1: 100,000,000-200,000,000) without sorting bam file. Any idea related with this would be appreciated.
              You should start a new thread.

              Having said that, a small python/perl/whatever script could do this (you could even put together a shell script, if you're so inclined). Just filter the output of samtools view through it.
              Last edited by dpryan; 09-24-2013, 05:27 AM.

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              • #8
                Originally posted by bioinfo816 View Post
                I need suggestion to extract the chromosome or chromosome region (e.g. chr1: 100,000,000-200,000,000) without sorting bam file. Any idea related with this would be appreciated.
                A more lazy alternative as suggested by swbarnes2 in this thread: http://seqanswers.com/forums/showthread.php?t=14702

                Comment

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