288 Add an excess alleles param #7221
Conversation
RoriCremer
force-pushed
the
rc-288-excess-alleles-param
branch
3 times, most recently
from
529244f to
c83e99c
Compare
| @@ -65,6 +65,12 @@ | |||
| optional = true) | |||
| protected double hqGenotypeABThreshold = 0.2; | |||
|
|
|||
| @Argument( | |||
| fullName = "excess-alleles-threshold", | |||
| doc = "excess alleles threshold", // TODO what even is this?!??! | |||
There was a problem hiding this comment.
something like "number of non-reference alleles above which a site will be filtered out." ?
also @kcibul should we add an option to NOT filter these at all? maybe by setting this to +Inf or something?
There was a problem hiding this comment.
I'd say that's a nice to have... by having the threshold we are more configurable than before AND we can effectively disable it by setting this to a very large number.
|
maybe this is in progress but can you add a corresponding optional input to the GvsCreateFilterSet wdl? |
| @@ -65,6 +65,12 @@ | |||
| optional = true) | |||
| protected double hqGenotypeABThreshold = 0.2; | |||
|
|
|||
| @Argument( | |||
| fullName = "excess-alleles-threshold", | |||
| doc = "excess alleles threshold", // TODO what even is this?!??! | |||
There was a problem hiding this comment.
I'd say that's a nice to have... by having the threshold we are more configurable than before AND we can effectively disable it by setting this to a very large number.
RoriCremer
force-pushed
the
rc-288-excess-alleles-param
branch
from
a224901 to
66d2466
Compare
|
Travis reported job failures from build 33966
|
I'm sure there is a better solution here, but wasn't sure of best practices
RoriCremer
force-pushed
the
rc-288-excess-alleles-param
branch
from
653f75c to
25a9d82
Compare
Dont just use the default of 6--pass a param for the value instead (in the wdl and gatk tool)
I ran a smoke test and the filtering completed successfully, but I'm not totally sure how to make sure it used the passed in param over the default. How can I check this?