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Old 10-17-2014, 03:02 AM   #7
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Location: Germany

Join Date: Apr 2012
Posts: 215

Ok, maybe the following helps...

1) Is there a particular reason for using the "-T" parameter. I never use it and I actually don't what it is useful for. Although it don't think it will change anything, you could try the conversion without that.

2) Your "GC01.concordant_uniq" file is a sam file created from one of the bam files using samtools view -h file.sam > GC01.concordant_uniq, isn't it? A more accurate comparison would be to use "diff file1 file2". If the output is empty, your files are equal.

3) If (1) doesn't help and (2) doesn't give you enough confidence, upgrade samtools to version 1.1 and check if the warning remains.
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