I am struggling with the Germline Pipeline available from the Algorithm_Commons workspace on Firehose. All of the samples I am trying to process with this workflow were sequenced at the Broad, either through the CRSP or the Picard pipelines. The samples fail at the "Single Sample VCFtoMAF" step (the last step of the workflow) because each of these samples has, according to the task, an 'invalid codon'. I've attached an example of the error message below.
I've been stumped with this problem for a couple of days now, and I've talked to multiple people involved in Firehose help. Ultimately, I cannot seem to fix this problem easily without altering the task itself. Is there something wrong with my samples? Something wrong with the task itself? Has anyone else experienced this problem? Any help and/or advice would be much appreciated. Thank you!