From: Anton K. <ant...@go...> - 2011-05-30 10:23:46
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Hi, 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: ~/samtools-0.1.12a/samtools view -h -b -F 0xC -f 0x3 input.bam -o ~/foobar.bam Now I want to remove duplicates... ~/samtools-0.1.12a/samtools rmdup ~/foobar.bam ~/rmdupped.bam ...and get this: [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? I am using samtools version Version: 0.1.12a (r862). Any help would be much appreciated. Thanks. Anton |