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Gavin Oliver
Dec 8, 2012, 2:04:49 PM12/8/12
to jointsnvmix...@googlegroups.com
Hi,
Apologies if this has been asked elsewhere. I am wondering if JSM2 utilizes duplicate marked reads in variant calling or whether it has some means of automatically dealing with them?
Best,
Gavin
aroth
Dec 8, 2012, 2:49:53 PM12/8/12
to JointSNVMix User Group
Hi Gavin,
Nothing in my code explicitly filters out duplicate flagged reads. I
usually just remove the duplicate reads instead of flagging them. If
this is a feature you are interested in though feel free to add it on
the issue tracker http://code.google.com/p/joint-snv-mix/issues/list.
Cheers,
Andy
Nothing in my code explicitly filters out duplicate flagged reads. I
usually just remove the duplicate reads instead of flagging them. If
this is a feature you are interested in though feel free to add it on
the issue tracker http://code.google.com/p/joint-snv-mix/issues/list.
Cheers,
Andy
Gavin Oliver
Dec 8, 2012, 3:18:37 PM12/8/12
to andrew...@gmail.com, JointSNVMix User Group
No worries at all - I just wanted to double check.
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