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 https://software.broadinstitute.org/firecloud/documentation/freecredits

Unified Genotyper: No Haplotype score annotated for indels.

Howdy,

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

Best Answer

Answers

Sign In or Register to comment.