HaplotypeCaller with WARNNING DepthPerSampleHC

Hello, sorry for my bad English.
While running GATK 4.0.1.1 Haplotypecaller with two or more bams together, this tool would send lots of lines of warning message about DepthPerSampleHC like follows:

10:32:58.674 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
10:33:02.097 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
10:33:02.102 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
10:33:02.114 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null

And all those messages are gone while using "--annotation-group StandardAnnotation", which will remove "DP" in format. Maybe it due to the "./." genotype in some samples.
So, could I keep "DP" in vcf.gz without receiving too many WARN ?
Many thanks!

Here is my running command :

gatk HaplotypeCaller --java-options -Xmx40g 
-R GRCh37_latest_chr_genomic.fna 
--dbsnp All_20170710.vcf.gz 
-O pop.vcf.gz 
-I B1700.refine.bam 
-I NC.refine.bam 
--standard-min-confidence-threshold-for-calling 30 
1>pop.HaplotypeCaller.log 

Best Answers

Answers

  • YangyxtYangyxt Member

    OMG, finally I got the access to post a comment. I just would like to know for this tip statement "WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null", what does it mean? I know it's a statement to inform users about issues happening during the process. But what does it specifically mean? What specific situation are we encountering when I see this tip.

  • YangyxtYangyxt Member

    We know this is a tip statement to inform users about issues happening during the whole process. I just would like to consult that what does this tip "WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null" specifically mean? What are we encountering when facing this tip??

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