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Producing GVCF with Haplotype Caller 3.3.0 - Incompatibility with stand_emit_conf & stand_call_conf?
I am using HC 3.3-0-g37228af to generate GVCFs, including the parameters (full command below):
The process completes fine, but when I look at the header of the gvcf produced, they are shown as follows:
After trying various tests, it appears that setting these values is incompatible with -ERC GVCF (which requires "-variant_index_type LINEAR" and "-variant_index_parameter 128000" )
1) Can you confirm if this is expected behaviour, and why this should be so?
2) Is this another case where the GVCF is in intermediate file, and hence every possible variant is emitted initially?
3) Regardless of the answers above, is stand_call_conf equivalent to requiring a GQ of 30?
java -Xmx11200m -Djava.io.tmpdir=$TMPDIR -jar /apps/GATK/3.3-0/GenomeAnalysisTK.jar \ -T HaplotypeCaller \ -I /E000007/target_indel_realignment/E000007.6.bqsr.bam \ -R /project/production/Indexes/samtools/hsapiens.hs37d5.fasta \ -et NO_ET \ -K /project/production/DAT/apps/GATK/2.4.9/ourkey \ -dt NONE \ -L 10 \ -A AlleleBalance \ -A BaseCounts \ -A BaseQualityRankSumTest \ -A ChromosomeCounts \ -A ClippingRankSumTest \ -A Coverage \ -A DepthPerAlleleBySample \ -A DepthPerSampleHC \ -A FisherStrand \ -A GCContent \ -A HaplotypeScore \ -A HardyWeinberg \ -A HomopolymerRun \ -A ClippingRankSumTest \ -A LikelihoodRankSumTest \ -A LowMQ \ -A MappingQualityRankSumTest \ -A MappingQualityZero \ -A MappingQualityZeroBySample \ -A NBaseCount \ -A QualByDepth \ -A RMSMappingQuality \ -A ReadPosRankSumTest \ -A StrandBiasBySample \ -A StrandOddsRatio \ -A VariantType \ -ploidy 2 \ --min_base_quality_score 10 \ -ERC GVCF \ -variant_index_type LINEAR \ -variant_index_parameter 128000 \ --GVCFGQBands 20 \ --standard_min_confidence_threshold_for_calling 30 \ --standard_min_confidence_threshold_for_emitting 10