Hello,
We have been comparing whole genome sequence bam files and we have found
that samtools sort -n either removes or modifies the reads as it sorts. We
have tried it on both the older version and version 1.0 and have had the
same results. We found that several reads are in our original file, but
after sorting they are no longer there. I am not sure as to what could be
causing this. We have checked to make sure that we are running the program
as specified in the specs. We have not gone into the source code to try
and identify the problem. We have run it several times with consistent
results. Any help or advice is welcomed.
Thanks,
Mark
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