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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?


Comments (4)


I known that this question should not post to the GATK forum because the ERROR told me that "Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself." However, I really cant find which step I made this error although I have read many documentations of GATK forum about this error. Could you please give me some suggestions? Much thanks!!

In my VCF file, I find that not all the SNP terms have the same set of annotation, and some annotations cant be found in some SNP terms, like this:

chr1    5036777 rs898335        T       G       36.74   .       AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLE AF=1.00;MQ=37.00;MQ0=0;QD=18.37  GT:AD:DP:GQ:PL  1/1:0,2:2:6:64,6,0
chr1    9507566 rs12742542      T       C       33.74   .       AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.00;MQ0=0;QD=16.87   GT:AD:DP:GQ:PL  1/1:0,2:2:6:61,6,0
chr1    9507621 rs12755964      G       A       37.74   .       AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.00;MQ0=0;QD=18.87   GT:AD:DP:GQ:PL  1/1:0,2:2:6:65,6,0
chr1    22376947        rs2473327       A       G       40.74   .       AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.00;MQ0=0;QD=20.37   GT:AD:DP:GQ:PL  1/1:0,2:2:6:68,6,0
chr1    38061706        rs10908362      G       C       32.74   .       AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.00;MQ0=0;QD=16.37   GT:AD:DP:GQ:PL  1/1:0,2:2:6:60,6,0
chr1    78317717        rs10782656      G       C       36.74   .       AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.00;MQ0=0;QD=18.37   GT:AD:DP:GQ:PL  1/1:0,2:2:6:64,6,0
chr1    111457142       rs1282019       A       G       35.74   .       AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=30.81;MQ0=0;QD=17.87   GT:AD:DP:GQ:PL  1/1:0,2:2:6:63,6,0
chr1    121484153       rs9701684       C       G       32.74   .       AC=2;AF=1.00;AN=2;DB;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=19.48;MQ0=3;QD=6.55    GT:AD:DP:GQ:PL  1/1:2,3:5:6:60,6,0
chr1    121484423       rs7368003       T       C       83.03   .       AC=2;AF=1.00;AN=2;DB;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=28.24;MQ0=1;QD=16.61   GT:AD:DP:GQ:PL  1/1:0,5:5:12:111,12,0
chr1    121484503       rs4898086       T       A       311.77  .       AC=2;AF=1.00;AN=2;DB;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=33.63;MQ0=1;QD=25.98  GT:AD:DP:GQ:PL  1/1:0,12:12:33:340,33,0
chr1    121484591       rs4898109       T       A       463.77  .       AC=2;AF=1.00;AN=2;DB;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.9947;MLEAC=2;MLEAF=1.00;MQ=30.44;MQ0=1;QD=23.19  GT:AD:DP:GQ:PL  1/1:0,20:20:54:492,54,0
chr1    121484599       rs4898111       C       G       109.77  .       AC=1;AF=0.500;AN=2;BaseQRankSum=-0.555;DB;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=4.9775;MLEAC=1;MLEAF=0.500;MQ=30.78;MQ0=1;MQRankSum=-1.030;QD=5.23;ReadPosRankSum=1.664       GT:AD:DP:GQ:PL  0/1:14,7:21:99:138,0,312
chr1    121484600       rs1825267       T       C       100.77  .       AC=1;AF=0.500;AN=2;BaseQRankSum=-1.347;DB;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=4.9775;MLEAC=1;MLEAF=0.500;MQ=30.78;MQ0=1;MQRankSum=-1.743;QD=4.80;ReadPosRankSum=1.585       GT:AD:DP:GQ:PL  0/1:14,7:21:99:129,0,310
chr1    121484602       rs74187930      T       C       190.77  .       AC=1;AF=0.500;AN=2;BaseQRankSum=1.323;DB;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=4.9775;MLEAC=1;MLEAF=0.500;MQ=31.09;MQ0=1;MQRankSum=1.323;QD=8.67;ReadPosRankSum=-2.306        GT:AD:DP:GQ:PL  0/1:10,11:22:99:219,0,223
chr1    121484650       rs4092774       A       G       58.77   .       AC=1;AF=0.500;AN=2;BaseQRankSum=-1.620;DB;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=30.73;MQ0=2;MQRankSum=-0.540;QD=3.92;ReadPosRankSum=-0.231      GT:AD:DP:GQ:PL  0/1:10,4:15:87:87,0,222

e.g. MQRankSum can be found only in the last 4 terms.

and my Command Line:

java -Xmx15g -jar /ifs1/ST_POP/USER/lantianming/HUM/bin/GenomeAnalysisTK-2.7-2-g6bda569/GenomeAnalysisTK.jar 
    -glm BOTH 
    -l INFO 
    -R /nas/RD_09C/resequencing/soft/pipeline/GATK/bundle/2.5/hg19/ucsc.hg19.fasta 
    -T UnifiedGenotyper 
    -I /ifs1/ST_POP/USER/lantianming/HUM/align/bwa/recal_03/test.realn_8.recal.bam 
    -D /nas/RD_09C/resequencing/soft/pipeline/GATK/bundle/2.5/hg19/dbsnp_137.hg19.vcf 
    -o /ifs1/ST_POP/USER/lantianming/HUM/align/bwa/callsnp/realn_8.recal.bam.vcf
    -metrics /ifs1/ST_POP/USER/lantianming/HUM/align/bwa/callsnp/snpcall.metrics

What can I do to solve this problem?

Thanks a lot !

Comments (4)

I have a set of VCFs with identical positions in them:

VCF1: 1 10097 . T . 26 . AN=196;DP=1622;MQ=20.06;MQ0=456 GT:DP

VCF2: 1 10097 . T . 21.34 . AN=198;DP=2338;MQ=19.53;MQ0=633 GT:DP

VCF3: 1 10097 . T . 11.70 . AN=240;DP=3957;MQ=19.74;MQ0=1085 GT:DP

VCF4: 1 10097 . T . 15.56 . AN=134;DP=1348;MQ=18.22;MQ0=442 GT:DP

If I use all of them as input for VariantRecalibrator, which annotations will VariantRecalibrator use? Should I instead merge the VCFs with CombineVariants and run VariantAnnotator, before I run VariantRecalibrator?

I'm not sure if the forum is for asking technical questions only or you are allowed to ask for best practices as well. Feel free to delete my question, if it doesn't belong here. Thank you.