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  • BWA mapping against hg18

    Has anyone completed successfully mapping against hg18 genome? How did you build the index and followed by mapping. I am getting segmentation fault even after checking out from svn about the latest release.
    Please let me know the details.
    Thanks.

  • #2
    I don't have the most recent BWA release, but I've built & aligned several Illumina datasets to hg18

    Have you checked to make sure your FASTA file of hg18 isn't corrupt? Perhaps the index builder is intolerant of something as trivial as whether there are blank lines or if the last line is terminated with a newline. Also make sure there is nothing before the first header line & that every header line is correct (no spaces either side of the angle bracket).

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    • #3
      Originally posted by seq_GA View Post
      Has anyone completed successfully mapping against hg18 genome? How did you build the index and followed by mapping. I am getting segmentation fault even after checking out from svn about the latest release.
      Please let me know the details.
      Thanks.
      Please, make sure you use the latest version of bwa (or svn).
      Post here what version you use and how you got it. There is a very recent post
      with the same problem.
      I think there is an old link somewhere that points to older versins of bwa and people uses that.
      -drd

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      • #4
        Also check were you got the fasta files from. Some include all the unmapped super-contigs that make the file to big for the index step.

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        • #5
          How big is your memory. and which index algorithm you used, is or bwtsw? I used "is" to index hg19 before, also got segmentation fault message. Then I switched to "bwtsw".
          Originally posted by seq_GA View Post
          Has anyone completed successfully mapping against hg18 genome? How did you build the index and followed by mapping. I am getting segmentation fault even after checking out from svn about the latest release.
          Please let me know the details.
          Thanks.

          Comment


          • #6
            When I build the index using bwtsw, I don't get any errors. I get the error only during bwa sampe stage. I have already explained about the errors in one of my other thread. I have no idea why this is happening. I have checked out from svn and still get the same error. Thanks.

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            • #7
              I also got the segmentation fault when using version 0.5.7. (Even when I ran a very small file with 10 reads). So when I changed to version 0.5.6 everything went fine. Maybe you could give this a try

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              • #8
                Ok thx for the info. I will try.

                Comment

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