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broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool
GNU General Public License v2.0
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Is it necessary to mark/remove duplicates before using pilon? #70

Closed zengxiaofei closed 5 years ago

zengxiaofei commented 6 years ago

I notice the option --duplicates in pilon:

Use reads marked as duplicates in the input BAMs (ignored by default).

From my understanding, when some reads were marked as duplicates, pilon will ignore these reads. So if I want to prevent the interference caused by PCR, is it necessary to mark these duplicates or remove them from the BAM file before using pilon?

Thank you!

Xiaofei

w1bw commented 5 years ago

Sorry, I'm catch up on some very old pilon maintenance requests. If you are detail with PCR amplified libraries, especially from low input, it's probably best to mark the duplicates.