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HaplotypeScore not generated?
We're trying to run HaplotypeCaller with some additional annotations. For reference, here's the command we're using:
java -Xmx16g -jar GenomeAnalysisTK.jar -R GRCh37.fa -T HaplotypeCaller -A ReadPosRankSumTest -A RMSMappingQuality -A ClippingRankSumTest -A HaplotypeScore -A MappingQualityRankSumTest -o calls.vcf -I input.bam -nct 24
We're seeing ReadPosRanksum, Clippingranksum, and MQRanksum generated with our calls, but we're not seeing HaplotypeScore. Is HaplotypeScore only generated for certain variants? Does it depend on some other options that we're not using?