To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

Producing GVCF with Haplotype Caller 3.3.0 - Incompatibility with stand_emit_conf & stand_call_conf?

SteveLSteveL BarcelonaMember
edited February 2015 in Ask the GATK team

I am using HC 3.3-0-g37228af to generate GVCFs, including the parameters (full command below):

stand_emit_conf 10
stand_call_conf 30

The process completes fine, but when I look at the header of the gvcf produced, they are shown as follows:

standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0

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$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
Post edited by SteveL on

Best Answers


  • SteveLSteveL BarcelonaMember

    @Geraldine_VdAuwera said:
    That's right, as we've pointed out previously, when you run HC in GVCF mode the thresholds are set to 0 automatically since we want to account for every possibility. The thresholds are applied later when doing the joint genotyping. Note that they apply to the site-level QUAL, not to the genotype quals.

    Thanks both - I tried to comment just before original poster replied, but my comments aren't coming through

Sign In or Register to comment.