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:
Now I want to remove duplicates...
...and get this:
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.
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
Code:
~/samtools-0.1.12a/samtools rmdup ~/foobar.bam ~/rmdupped.bam
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
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.
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