1 answer
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my mistake I thought you asked about the samtools fixmate, I think the picard version does something similar
If you consult both the samtools documentation and the SAM specification
http://samtools.sourceforge.net/samtools.shtml
http://samtools.sourceforge.net/SAM1.pdf
You will find that mate paired reads have several attributes that may be computed. For example columns 7 and 8, tags such as MQ, Q2 and R2 and probably others.
The fixmate command will attempt to fill in these attributes. There are some details to keep in mind. The file needs to be sorted by read name and this also implies that your read naming was such that this operation places mate pairs next to one another in the file.
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