-
Notifications
You must be signed in to change notification settings - Fork 14
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Implement Tumor-Normal pair somatic variant calling #133
Labels
Comments
Things to add/change:
|
mfoll
referenced
this issue
Oct 15, 2016
nalcala
added a commit
that referenced
this issue
Oct 17, 2016
This was referenced Oct 20, 2016
nalcala
added a commit
that referenced
this issue
Oct 21, 2016
…nomial distribuation (for issue #133)
tdelhomme
referenced
this issue
Oct 24, 2016
This issue was closed.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
We should add a feature for calling somatic mutations from multiple pairs of tumor-normal.
The basic idea will be to calculate for each normal sample the qvalue we would have if there were a mutation with AF=20%. We call that QVAL_20PC and add it in the genotype filed for all samples (put "." for tumors). Using this, we can classify mutations in the tumor as SOMATIC, GERMLINE or UNKNOWN and write this as a new genotype field (SOMATIC_STATUS):
QVAL_20PC should always be calculated in case we change the threshold afterward.
All normals will have "." as SOMATIC_STATUS.
If QVAL_TUMOR<50 put "." as SOMATIC_STATUS.
EDIT: Also flag tumors when low power to detect a mutation with AF=X%
The text was updated successfully, but these errors were encountered: