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

CNV PerformAlleleFractionSegmentation: Shl doc perform allele fraction segmentation #1119

Closed sooheelee closed 7 years ago

sooheelee commented 7 years ago
sooheelee commented 7 years ago

Nope, botched commit in attempt to rename my local branch.

sooheelee commented 7 years ago

Hey @LeeTL1220, is there a way to only keep the changes to PerformAlleleFractionSegmentation.java? I have other branches for the changes in the other two files.

sooheelee commented 7 years ago

I will redo this.

samuelklee commented 7 years ago

No example command since there is no WDL for me to reference. FYI @LeeTL1220 @achevali.

There is no WDL because this tool is experimental. In general, you should be able to put together example command lines from the integration tests for a tool.

tag doc and mention that the tumorHets file is from GetHetCoverage.

We should probably say that the tumorHets file is from GetBayesianHetCoverage, preferably, but can also come from GetHetCoverage.

samuelklee commented 7 years ago

Oops, just saw that you closed this, @sooheelee! Just so you know, you could've removed the unwanted files using git.