Avatar

L. A. Liggett

  • Total activity 13
  • Last activity
  • Member since
  • Following 0 users
  • Followed by 0 users
  • Votes 0
  • Subscriptions 4

Comments

Recent activity by L. A. Liggett Sort by recent activity Recent activity Votes
  • Bhanu Gandham it looks like this error can be solved by passing `--max-mnp-distance 0` when building the panel of normals. However, this option is not available in the best practices workflow that ...

  • Thanks Bhanu Gandham, I did upload (named `liggett_3_12_20.zip`) the vcf and index with the error log since it looks to me that the error is in processing chr10:60784794 from the vcf. Does this wor...

  • David Benjamin This seems to have fixed the issue. The job has been running for 2.5 hours at this point so hopefully works. Thanks.

  • David Benjamin I am running the WDL, not an associated jupyter notebook. And I am setting the gatk_docker to `workspace.gatk_docker`. And the field isn't suggesting an input for the 4.1.5.0 docker;...

  • David Benjamin It looks like the workspace I'm using was updated to 4.1.4.1. And I'm using v2.7.0 of the Mutect2_PON, but I do not see any way of adjusting the GATK version. Is this something that ...