-m flag vs NC from info field

zeeev / wham

Structural variant detection and association testing

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-m flag vs NC from info field #24

Closed abolia closed 8 years ago

abolia commented 8 years ago

Hi Zev,

Can you please help me understand how are the "-m" flag and "NC" related. To my knowledge, both relate to the # of soft clipped required at the breakpoint. I am using -m flag (minimum number of soft-clips supporting START) as 15 while running WHAM but I see that most of my calls still have NC < 15. It shouldn't actually report any SV that has soft clips collapsed into the consensus that are less than 15. Can you please clarify this one for me.

Thanks for your help.

Ashini

zeeev commented 8 years ago

@abolia Thank you for pointing out the bug. I've fixed it. Let me know if you have any more problems.

The changes are in the repo.

abolia commented 8 years ago

Great.

Thanks, Ashini