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GATK HaplotypeCaller3.4 warnings

tommycarstensentommycarstensen United KingdomMember ✭✭✭
edited May 2015 in Ask the GATK team

GATK3.4 is throwing lots of warnings. Should I be concerned about any of them?

I'm not sure, which --variant_index_type to set, so I will make sure to use the correct file extension going forward:

WARN  17:02:08,480 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter 
WARN  17:02:08,484 GATKVCFUtils - Creating Tabix index for out_HaplotypeCaller/20/APP5339451.vcf.gz, ignoring user-specified index type and parameter 

I also got this warning with earlier versions:

WARN  17:02:10,495 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation 

Is this something to be concerned about?

WARN  17:02:18,771 PairHMMLikelihoodCalculationEngine$1 - Failed to load native library for VectorLoglessPairHMM - using Java implementation of LOGLESS_CACHING 

I didn't ask for these annotations:

WARN  17:02:19,078 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper 
WARN  17:02:19,079 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line. 

My command line looked like this:

-A Coverage -A FisherStrand -A StrandOddsRatio -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest

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