Hi,
I am trying to run samtools rmdup on a bam file and I get the following error messages.
I googled and didn't find anything on that, so I hope that someone here might be able to help me.
edit: just some additional info. I mapped 100 bp PE Illumina reads with stampy&bwa.
I am trying to run samtools rmdup on a bam file and I get the following error messages.
[bam_rmdup_core] inconsistent BAM file for pair 'HWI-ST1027:65: D03FGACXX:4:2107:2691:8134'. Continue anyway.
[bam_rmdup_core] inconsistent BAM file for pair 'HWI-ST1027:65: D03FGACXX:4:2208:17576:79909'. Continue anyway.
[bam_rmdup_core] inconsistent BAM file for pair 'HWI-ST1027:65: D03FGACXX:4:2301:18313:189015'. Continue anyway.
[bam_rmdup_core] inconsistent BAM file for pair 'HWI-ST1027:65: D03FGACXX:4:2307:15133:98183'. Continue anyway.
[bam_rmdup_core] inconsistent BAM file for pair 'HWI-ST1027:65: D03FGACXX:4:2301:4254:2861'. Continue anyway.
[bam_rmdup_core] inconsistent BAM file for pair 'HWI-ST1027:65: D03FGACXX:4:2208:17576:79909'. Continue anyway.
[bam_rmdup_core] inconsistent BAM file for pair 'HWI-ST1027:65: D03FGACXX:4:2301:18313:189015'. Continue anyway.
[bam_rmdup_core] inconsistent BAM file for pair 'HWI-ST1027:65: D03FGACXX:4:2307:15133:98183'. Continue anyway.
[bam_rmdup_core] inconsistent BAM file for pair 'HWI-ST1027:65: D03FGACXX:4:2301:4254:2861'. Continue anyway.
edit: just some additional info. I mapped 100 bp PE Illumina reads with stampy&bwa.
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