Unified Genotyper: No Haplotype score annotated for indels.
I used UnifiedGenotyper from version GenomeAnalysisTK-2.4-9-g532efad and Indels were not annotated with Haplotype score while SNVs were. when I went to perform VariantRecalibration on the Indels, it choked saying that none of the records had indels annotated in the raw VCF. I poked around and didn't see this being a bug previously reported for UG (although I'm surprised that nobody else has come across this yet).
below is an example line from the output. first record is an SNV, second is an indel;
1 28588 . G T 33.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.978;DP=19;Dels=0.00;FS=2.632;GC=39.40;HaplotypeScore=6.9577;MLEAC=1;MLEAF=0.500;MQ=28.03;MQ0=8;MQRankSum=-1.106;QD=1.78;ReadPosRankSum=-0.978 GT:AB:AD:DP:GQ:PL 0/1:0 .790:15,4:19:62:62,0,216 1 28590 . T TTGG 283.73 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.666;DP=18;FS=0.000;GC=39.40;MLEAC=1;MLEAF=0.500;MQ=28.80;MQ0=0;MQRankSum=1.179;QD=5.25;ReadPosRankSum=0.067 GT:AD:DP:GQ:PL 0/1:2,7:11:32:321,0,32
below is the command line for UG;
java -jar $GATK_DIR/GenomeAnalysisTK.jar \ -T UnifiedGenotyper \ -R $REF_GENOME \ --input_file /$CORE_PATH/$PROJECT/BAM/Aggregate/$SM_TAG".bam" \ --dbsnp /isilon/sequencing/GATK_resource_bundle/2.2/b37/dbsnp_137.b37.vcf \ -L $WG_BED \ -glm BOTH \ -A QualByDepth \ -A HaplotypeScore \ -A MappingQualityRankSumTest \ -A ReadPosRankSumTest \ -A FisherStrand \ -A GCContent \ -A AlleleBalanceBySample \ -o $CORE_PATH/$PROJECT/temp/$SM_TAG".raw.UG.vcf" \ -nt 4