Take a look at this <https://github.com/samtools/samtools/issues/359> git
issue page. Does the last comment address your situation?
If not, it may be helpful to grep out all lines in your pre-rmdup bam file
for read pair "xxxxxx", to give us an example.
~Joe
On Wed, Aug 30, 2017 at 12:36 AM, Qian Li <liqian.p...@gmail.com> wrote:
> Hi Admin,
>
> I used rmdup within samtools to remove duplicates for paired-end reads
> with default parameters, and met with this warning [bam_rmdup_core]
> inconsistent Bam file for pair “xxxxxx”. Continue anyway.
>
> I have trimmed the fastq files according to known adapter, and kept the
> co-existing read pairs, so the length of read is shorter and may be
> different for mate 1 and 2 reads, then run mapping, sort the bam files by
> position. Is the warning caused by this trimming step?
>
> Thank you.
>
> Best,
> Li Qian
>
>
>
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--
Joseph Fass
Bioinformatics Data Analyst
UC Davis Genome Center - Bioinformatics Core
http://bioinformatics.ucdavis.edu/
jnf...@ucdavis.edu
phone ~ 530.752.2698
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