rgcgithub / clamms

CLAMMS is a scalable tool for detecting common and rare copy number variants from whole-exome sequencing data.

Other

29 stars 10 forks source link

Error executing CLAMMS: ERROR: more than 4096 CNVs detected! #22

Open lakhujanivijay opened 4 years ago

lakhujanivijay commented 4 years ago

ERROR: more than 4096 CNVs detected!
The reference panel must not be a good fit for this sample.
Note: CLAMMS is not meant to be used with cancer samples.

I could not understand what is this error. Can you please help ?

lakhujanivijay commented 4 years ago

It has to do something with this:

define CNV_BUF_SIZE 4096

https://github.com/rgcgithub/clamms/blob/f486d6b2dcb54c2f579592f62c9ed6642434cf70/call_cnv.c#L13

katherinef commented 4 years ago

I'm guessing there is a maximum number of expected CNVs per sample. In their publications, they seem to call a median of 14 "unfiltered" CNVs per sample. Strangely, I am also getting far more than this (though not as many as 4096). Did you manage to resolve this problem?