GE
- Total activity 32
- Last activity
- Member since
- Following 0 users
- Followed by 0 users
- Votes 0
- Subscriptions 10
Comments
Recent activity by GE Sort by recent activity-
Thank you
-
Hi, This is the recommended best practices Mutect2 pipeline from Terra: https://app.terra.bio/#workspaces/help-gatk/Somatic-SNVs-Indels-GATK4/workflows/help-gatk/2-Mutect2-GATK4 https://dockstore.o...
-
Sure. Note that if others think this is useful, a compromise might be to add to the tag "NOT-USED", so that the description of the tag is still present, but the user also can see that it was not ap...
-
Thanks. That makes sense. The only part I think should be evaluated in future GATK versions is: "Regarding the VCF header, we do not change the header based on whether or not a certain filter was a...
-
I made it with Picard BedToIntervalList, so it must be option A. I would recommend GATK add auto-detection of format for intervals. interval_list, list, intervals as extensions can be confusing.
-
In a multi-sample analysis with 2 tumor samples vs 1 normal, if a somatic mutation is high quality in one of the tumor samples, but absent from the other tumor sample, will it be called? In other w...
-
Tool was Mutect2, and the interval list file was passed to the -XL command line option. I don't have the full stack trace anymore available.
-
Hi, I found the error. GATK is not correctly interpreting a file with the .intervals extension as an interval list format. Once I changed it to .interval_list it worked.
-
Actually I figured out the problem above. I was inputting the file as a GCP (gs://) URL, and for some reason, -XL is not able to accept that. I also had to rename the file as combinedblacklist.inte...
-
Documentation error: Intervals seems to be a required parameter for new databases. So it should be listed in the "Required Arguments" section.