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broadinstitute / gatk-sv

A structural variation pipeline for short-read sequencing
BSD 3-Clause "New" or "Revised" License
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Modification of parameters #651

Open andrewruttenberg opened 7 months ago

andrewruttenberg commented 7 months ago

Hello. I was wondering if there is any documentation on the role each parameter plays within the overall code. I am trying to use GATK-SV to identify de novo structural variants and thus want to be more lenient in calling SVs in the parents to reduce the false negative rate but I cannot find any information on how I can adjust the inputs to do so. Thank you very much.

mwalker174 commented 3 months ago

Hi @andrewruttenberg we are working on filtering documentation but you can reference my post over in #615 (if you're doing joint calling)