search

broadinstitute / gatk-protected

Obsolete/Legacy GATK repository -- go to https://github.com/broadinstitute/gatk instead
BSD 3-Clause "New" or "Revised" License
33 stars 20 forks source link

Limit the number of copy number states and designate a special state to capture all higher copy number states #1064

Closed mbabadi closed 7 years ago

mbabadi commented 7 years ago

At the moment, the maximum copy number in gCNV is set by the dimension provided transition matrices. One needs to work with copy number states up to 10 ~ 20 in order to capture high copy number states seen in certain regions.

It is desirable to limit the number of states, however, to designate a special state that represents _all copy number states at and above CNmax. This can be achieved by adjusting the emission probability to integrate over all higher copy number states. There are other challenges too (e.g. calculating copy number posteriors from such states).

droazen commented 7 years ago

Issue moved to broadinstitute/gatk #3001 via ZenHub