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  • Segmentation fault with samtools rmdup

    I am running into a Seg fault when using samtools rmdup.

    I have paired-end alignments from bwa and filter them so that I retain only those pairs which are actually pairs, which have both fragments properly aligned, with no fragment unmapped, and with no next fragment unmapped:

    Code:
    ~/samtools-0.1.12a/samtools view -h -b -F 0xC -f 0x3 input.bam -o ~/foobar.bam
    Now I want to remove duplicates...

    Code:
    ~/samtools-0.1.12a/samtools rmdup ~/foobar.bam ~/rmdupped.bam
    ...and get this:

    Code:
    [bam_rmdup_core] processing reference chr2...
    [...] (long output omitted, here it goes through the chromosomes)
    [bam_rmdup_core] processing reference chr2...
    [bam_rmdup_core] 1 unmatched pairs
    [bam_rmdup_core] processing reference chrX...
    Segmentation fault
    My questions are:

    What can I do about the Segmentation fault?

    Why does it report "1 unmatched pairs", I thought that through the previous filtering (see above) there can not be any unmatched pairs anymore? How can I identify the unmatched pair, if there really is one (I tried samtools view -f 0x4, that doesn't find anything though)?

    I am using samtools version Version: 0.1.12a (r862).

    Any help would be much appreciated. Thanks.

  • #2
    perhaps sort first?

    Have you tried sorting first?

    The samtools man page says:

    samtools rmdup [-sS] <input.srt.bam> <out.bam>

    Which implies that the input should be sorted.

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