Duplicated reads

[joshuashen]

Duplicated reads inflate quality scores of variants. samtools provides a command to remove apparent duplicated reads:

rmdup samtools rmdup Remove potential PCR duplicates: if multiple read pairs have identical external coordinates, only retain the pair with highest mapping quality. This command ONLY works with FR orientation and requires ISIZE is correctly set.

http://samtools.sourceforge.net/samtools.shtml