Jérémie Kalfon
Jérémie Kalfon
Hello @davidbenjamin , Why do you say they aren't meaningful? The phasing of a somatic mutations seems quite important to me. What about when I ask mutect2 to emit germlines...
@gbrandt6 this is the same as #6289 and as per my comment there. I still see the bug in gatk 4.2.6.1. It occurs rarely but breaks the pipelines.
just to help with associating issues: here is the list of issues that seems to be talking about the same problem: #6651, #7523, #6345, #4307, #6546, #3749, #4804, #6289. Seems...
I can, this only happens on 10 of our 2000 samples (only in WES) none of our 600 WGS seems to have the same issue. It is always on some...
my quickfix was to reduce the intervals to target regions of my WES (instead of using the full genome region) and give it to funcotator. Remark: The GATK mutect2 WDL...
After running it on all my samples it actually only solved half of them... I will look into the try/catch fix
Since I was able to use another fix (shared in #6651), I will not continue working on this PR for now. I have some deadlines unfortunately. FYI, I haven't had...
tested on one sample and it succeeded.
@jonn-smith this is tested on my end. would you mind testing on yours and reviewing the pull request? Also I am trying to run it using the jar file but...
Hello @jonn-smith, @droazen, would you be able to help on this or merge the request? Best,