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HaplotypeCaller - AD missing in output vcf file

mjlarsenmjlarsen Member
edited October 2012 in Ask the GATK team


After I switched from the UnifiedGenotyper to HaplotypeCaller, I've noticed that the AD information is now missing from the output vcf file - everything else seems to be there.

I use the following command:

$GATK HaplotypeCaller \
-o $SAMPLE.haplo.vcf \
-I $SAMPLE.marked.realigned.recal.bam \
--dbsnp $DBSNP \
-stand_call_conf 30.0 \
-stand_emit_conf 10.0 \
-A DepthPerAlleleBySample \
-A BaseQualityRankSumTest \
-A DepthOfCoverage \
-A FisherStrand \
-A HaplotypeScore \
-A MappingQualityRankSumTest \
-A MappingQualityZero \
-A QualByDepth \
-A ReadPosRankSumTest \
-A RMSMappingQuality

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