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jluebeck / FaNDOM

Fast Nested Distance aligner for Optical Maps
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About INDEL size from FaNDOM #7

Open chycheng2015 opened 2 years ago

chycheng2015 commented 2 years ago

Hello Jen

It seems that FaNDOM wrapper only detected INDEL>2kb. Is there any way to down the threshold by modifying your python script(s)?

Thank you, Cheng

chycheng2015 commented 2 years ago

Oh, I just found "dif = ref_dist - q_dist" in indel_detection_contigs.py. It seems you used dif for filtering. I will try to modify this number to call INDEL. Best, Cheng

jluebeck commented 2 years ago

Hi Cheng,

You are of certainly welcome to experiment with the code to try different minimum indel size cutoffs - but please keep in mind that optical map data has limits for which it cannot reliably resolve indels below a certain size. We have not done rigorous testing for values below 2kbp regarding the accuracy of such indel calls.

Thanks, Jens

chycheng2015 commented 2 years ago

Hi, Jen, Thanks so much for your comment. I am fully aware of the limit of optical map on detecting insdel under certain size, but I still want get some overall idea about the size limit of FaNDOM. Best, Cheng