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  • merging bwa alignments

    Hello,
    I am using bwa to map solid data to the mouse genome, but get a segmentation fault while running bwa aln. If I separate the genome into 2 halves, it works all right, so I assume that the segfault was a memory problem. My question is: Is there a way to merge the result of mapping to 2 halves of the genome?

    I have a similar question about dividing the reads into smaller subsets, while using the full database.

    I appreciate any help on this.

  • #2
    I've been doing BWA alignments and merging them using picard-tools "MergeSamFiles.jar"

    Comment


    • #3
      merging files which map reads to separate parts of the genome

      Thank you for you response. I have also used samtools merge.

      As I understand it, bwa eliminates reads that map to more than one place in the genome. Since my 2 files involves mapping reads to separate halves of the genome, reads that are mapped in both files should be eliminated. Does the merge process recognize this?

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      • #4
        No it does not.

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        • #5
          One should never split the genome. Split the read set. It is true for essentially all NGS aligners.

          Comment


          • #6
            Well, the reason I split the genome was that I ran into a segmentation fault running "bwa aln -c" against the entire mouse genome. I was able to isolate this to a single read. I tried it against various genomes, and it worked all right for smaller genomes, eg human mrna and half the mouse genome.

            Here is the problem read:
            @559_9_257_F3
            GNANNNGGGGGNNNNNCNNNAGCACGAGAANNNNCGNGNGNTNCNNCNN
            +
            2!'!!!)*'&)!!!!!&!!!')&&.*)&+'!!!!(,!&!)!'!&!!&!!

            I also assumed that there must be a way to postprocess a merged file from a split genome, although I haven't done it yet.

            Comment

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