GATK HaplotypeCaller3.4 warnings
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