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HaplotypeCaller could not produce HaplotypeScore in raw.vcf file

XiaominXiaomin Member
edited July 2013 in Ask the GATK team

Hi, I’m trying to use GATK(2.6-4) HaplotypeCaller for variant calling as follows:

 java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R hg19/ucsc.hg19.fasta -I 557_family_all_individuals.markdup.realigned.recal.sorted.bam --dbsnp hg19/dbsnp_137.hg19.vcf -o 557_family_all_individuals.raw.vcf -stand_call_conf 30.0 -stand_emit_conf 5.0 -maxAltAlleles --annotation HaplotypeScore --annotation MappingQualityRankSumTest --annotation FisherStrand --annotation ReadPosRankSumTest --annotation QualByDepth -log 557_family_all_individuals.HaplotypeCaller.log

I found there is no HaplotypeScore in output raw.vcf file as follows:

 chrM    10399   .       G       A       525.58  .       AC=6;AF=1.00;AN=6;DP=19;FS=0.000;MLEAC=6;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.66     GT:AD:GQ:PL     1/1:0,8:24:232,24,0     1/1:0,1:3:30,3,0    1/1:0,10:30:289,30,0
 chrM    10820   .       G       A       1342.91 .       AC=6;AF=1.00;AN=6;DP=47;FS=0.000;MLEAC=6;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.57     GT:AD:GQ:PL     1/1:0,19:57:551,57,0    1/1:0,7:21:210,21,0 1/1:0,21:63:608,63,0
 chrM    10874   .       C       T       1630.90 .       AC=6;AF=1.00;AN=6;DP=58;FS=0.000;MLEAC=6;MLEAF=1.00;MQ=58.16;MQ0=0;QD=28.12     GT:AD:GQ:PL     1/1:0,20:60:580,60,0    1/1:0,12:36:360,36,01/1:0,25:75:717,75,0

So it could not pass the VariantRecalibrator step and stopped with the error massage "there is no HaplotypeScore in any input variant call set".

Can you tell me what the problem is? And how to fix this?

Thank you, Xiaomin

Post edited by Geraldine_VdAuwera on
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