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galaxyproject / tools-iuc

Tool Shed repositories maintained by the Intergalactic Utilities Commission
https://galaxyproject.org/iuc
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Picard MarkDuplicates: OPTICAL_DUPLICATE_PIXEL_DISTANCE #4500

Open helipiisk opened 2 years ago

helipiisk commented 2 years ago

I am using "MarkDuplicates" (2.18.2.2) to remove duplicates from my sequencing datasets coming from NovaSeq. From Picard documentation it suggests the OPTICAL_DUPLICATE_PIXEL_DISTANCE to be 2500 for NovoSeq, but the tool allows only up to 500. I asked also from Illumina and they confirmed, that it should be 2500.

https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard

bernt-matthias commented 2 years ago

@helipiisk could you open a pull request? You can just change the value here https://github.com/galaxyproject/tools-iuc/blob/92e89c89178482870c14cf15f38fbfd4470aa130/tools/picard/picard_MarkDuplicates.xml#L59

helipiisk commented 2 years ago

Thank you! Interestingly, it did not make any difference to my data compared with the value 500.