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  • problems with bam file and mpileup

    Hello everyone:

    I have a problem with samtools' mpileup.
    Im trying to map a set of reads (only 1 library for now) against a reference genome, to find SNPs. The command line I used is:

    $ samtools mpileup -uD -f ref_genome.fasta library.sorted.bam | bcftools view -bvcg library.raw.bcf

    the output I get is this:

    open: No such file or directory
    [mpileup] 1 samples in 1 input files
    Segmentation fault

    i dont know what's wrong. I used this same command line with other data and it worked just fine, so I could use some help.

    thank you!

  • #2
    Does "ref_genome.fasta" indexed?
    -f FILE faidx indexed reference sequence file [null]

    Comment


    • #3
      yes, it is.

      I run this command line earlier:

      $ samtools faidx ref_genome.fasta

      generating a ref_genome.fasta.fai file

      I don´t think that's the problem =(

      Comment


      • #4
        Fasta file chromosome names

        Hi, can you post the result of:

        Code:
        grep ">" ref_genome.fasta
        You can get these segfaults without message when your fasta header lines have spaces in them.

        Cheers,
        Paul

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

        Comment


        • #5
          Quick guess ...
          Shouldn't it be
          $ samtools mpileup -uD -f ref_genome.fasta library.sorted.bam | bcftools view -bvcg - > library.raw.bcf

          Comment


          • #6
            Thank you all!
            actually it was the missing "- >" before the "library.raw.bcf"
            thanks a lot!

            Comment

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