Question: V4 illumina Sequencer
gravatar for sbilobram
6.0 years ago by
sbilobram20 wrote:

We are currently using V4 Illumina Sequencers.  I am trying to estimate optical duplicates and to do so I have recently upgraded PicardTools to V 1.122 to enable readname abilty.  The generated metrics file now outputs a non-zero value for READ_PAIR_OPTICAL_DUPLICATES which seems reasonable.

When I change the option OPTICAL_DUPLICATE_PIXEL_DISTANCE in the PicardTool MarkDuplicate I get differing duplicate numbers of course.  For example if the option is left at default (100pixels) the tool returns 1111 optical duplicates for a particular BAM.  When i change the option to 10pixels the same BAM is shown to have 60 optical duplicates.

My question, what is the ideal pixel distance to set OPTICAL_DUPLICATE_PIXEL_DISTANCE to for this V4 generation of Illumina sequencer?  Is the default good enough?


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