Warnings should include info about their source
open | Created 2019-05-01 | Last updated 2019-05-15| Posted by aushev | See in Github


HaplotypeCaller bug


Feature request

HaplotypeCaller

When running HaplotypeCaller, I get tens of thousands of lines like the following:

13:02:04.113 WARN  DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
13:02:04.113 WARN  StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
13:02:04.113 WARN  DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
13:02:04.113 WARN  StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null

The problem is they are not informative: you can't tell what position/region caused them. Resulting repetitive messages are redundant.


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