288 Add an excess alleles param #7221
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RoriCremer
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| @@ -65,6 +65,12 @@ | |||
| optional = true) | |||
| protected double hqGenotypeABThreshold = 0.2; | |||
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| @Argument( | |||
| fullName = "excess-alleles-threshold", | |||
| doc = "excess alleles threshold", // TODO what even is this?!??! | |||
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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?
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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.
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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; | |||
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| @Argument( | |||
| fullName = "excess-alleles-threshold", | |||
| doc = "excess alleles threshold", // TODO what even is this?!??! | |||
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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
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Travis reported job failures from build 33966
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I'm sure there is a better solution here, but wasn't sure of best practices
RoriCremer
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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?