Anastasia

Trouble with newRecord "undeclared identifier" in bam

7

Hi, I'm having trouble initiating new records based on an old Bam file. My goal is to make modifications to certain fields (i.e mapping quality) based on criteria within a...

BaseRecalibratorSpark fails with "java.lang.IllegalArgumentException: Table1 1,3 not equal to 88,3"

6

## Bug Report ### Affected tool(s) or class(es) BaseRecalibratorSpark BQSRPipelineSpark ### Affected version(s) 4.1.0.0 ### Description We are running into a problem using BaseRecalibratorSpark. The tool fails soon after starting....