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GATK 3.7 HaplotypeCaller out vcf format

Hi everyone,

I just want to confirm what I got back from HaplotypeCaller (GATK 3.7) is correct format, it is VCF4.2 format, however, after following the best practice, I have a vcf file with the GT field with "/" not "|", according to the VCF4.2 format, the "/" means unphased genotype, however, haplotypeCaller should provide haplotype calls instead of genotypes right? Should I use the results as unphased or phased?

Here are couple lines from the vcf file generated.




1 10492 . C T 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.385;ClippingRankSum=0.000;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.37;MQRankSum=-1.282;QD=6.63;ReadPosRankSum=0.000;SOR=0.693 GT:AD:DP:GQ:PL 0/1:3,3:6:66:68,0,66

Thanks a lot!

Best Answer


  • SheilaSheila Broad InstituteMember, Broadie admin


    The genotype will have | only if it is in phase with another variant. In your example, that variant is not phased with another variant. Do you have an example of variants you think should be phased but are not?

    Can you post an example? Please include the BAM file and VCF records.


  • yzharoldyzharold Member

    Thanks for your explanation, the bam file was downloaded from 1000 Genomes Project, the famous NA12878 sample, it is a huge bam file from exome sequencing and mapped reads using illumina technology. I have used the following command to call the variants using HaplotypeCaller. I also attached the example vcf file to show multiple variants were called.

    Command line:

    java -Xmx10g -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R /pathto/reference -I /pathto/NA12878.bam -o raw.snps.indels.SIngleSample.vcf

    My assumption is that the HaplotypeCaller will not only call all the variants, but also provide the phased genotypes for each loci with "|" instead of "/" for this single sample?

    Sorry for the inconvenience, due to some limited uploading capability, I have to copy all the lines of variants called to give you an example, if it is not clear, I could email you the example I created (vcf) file with your the provided.



    1 10492 . C T 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.385;ClippingRankSum=0.000;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.37;MQRankSum=-1.2\
    82;QD=6.63;ReadPosRankSum=0.000;SOR=0.693 GT:AD:DP:GQ:PL 0/1:3,3:6:66:68,0,66
    1 14907 . A G 409.77 . AC=2;AF=1.00;AN=2;DP=16;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=26.34;QD=25.61;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,16:16:48\
    1 14930 . A G 580.77 . AC=2;AF=1.00;AN=2;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=25.54;QD=25.25;SOR=0.963 GT:AD:DP:GQ:PL 1/1:0,23:23:69\
    1 15118 . A G 27.75 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=23.55;QD=13.87;SOR=2.303 GT:AD:DP:GQ:PL 1/1:0,2:2:6:55,6,0
    1 50481 . GGT G 28.71 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=36.67;QD=14.35;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:65,6,0
    1 55299 . C T 57.28 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=46.36;QD=19.09;SOR=1.179 GT:AD:DP:GQ:PL 1/1:0,3:3:9:85,9,0
    1 104176 . C G 62.74 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=33.24;QD=31.37;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0
    1 104186 . T C 62.74 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=33.24;QD=31.37;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0
    1 104208 . C G 18.59 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0
    1 234481 . T A 36.74 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=34.48;QD=18.37;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:64,6,0
    1 255909 . A ATG 33.71 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=24.02;QD=16.85;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0
    1 528040 . C A 12.08 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.967;ClippingRankSum=0.000;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.96;MQRankSum=0.9\
    67;QD=4.03;ReadPosRankSum=0.000;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:21:40,0,21
    1 565286 . C T 2515.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.498;ClippingRankSum=0.000;DP=53;ExcessHet=3.0103;FS=30.881;MLEAC=2;MLEAF=1.00;MQ=22.45;MQRankSum=-6.\
    926;QD=34.24;ReadPosRankSum=0.164;SOR=7.784 GT:AD:DP:GQ:PL 1/1:2,48:50:76:2544,76,0
    1 565295 . A G 4468.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.614;ClippingRankSum=0.000;DP=142;ExcessHet=3.0103;FS=7.360;MLEAC=2;MLEAF=1.00;MQ=25.79;MQRankSum=-1.\
    442;QD=32.62;ReadPosRankSum=-1.599;SOR=0.676 GT:AD:DP:GQ:PL 1/1:2,135:137:99:4497,282,0
    1 565406 . C T 42.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.126;ClippingRankSum=0.000;DP=6;ExcessHet=3.0103;FS=3.979;MLEAC=1;MLEAF=0.500;MQ=36.79;MQRankSum=-0.6\
    74;QD=7.13;ReadPosRankSum=0.189;SOR=2.800 GT:AD:DP:GQ:PL 0/1:3,3:6:71:71,0,85
    1 565419 . C G 21.80 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.282;ClippingRankSum=0.000;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=43.00;MQRankSum=-0.2\
    53;QD=3.63;ReadPosRankSum=1.834;SOR=0.223 GT:AD:DP:GQ:PL 0/1:4,2:6:50:50,0,113
    1 567242 . G A 21.77 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0
    1 569933 . G A 52.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.652;ClippingRankSum=0.000;DP=7;ExcessHet=3.0103;FS=3.136;MLEAC=1;MLEAF=0.500;MQ=45.61;MQRankSum=0.84\
    2;QD=7.54;ReadPosRankSum=-0.484;SOR=0.916 GT:AD:DP:GQ:PL 0/1:4,3:7:81:81,0,102
    1 610242 . G A 23.79 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.060;ClippingRankSum=0.000;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.00;MQRankSum=0.00\
    0;QD=3.40;ReadPosRankSum=0.366;SOR=0.223 GT:AD:DP:GQ:PL 0/1:5,2:7:52:52,0,157
    1 663097 . G C 39.74 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.85;QD=19.87;SOR=2.303 GT:AD:DP:GQ:PL 1/1:0,2:2:6:67,6,0
    1 672209 . G A 21.77 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=39.00;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0

    Thanks a lot!

  • SheilaSheila Broad InstituteMember, Broadie admin


    Can you post the BAM file and bamout file for sites you think should be phased but are not?


  • yzharoldyzharold Member

    Hi Sheila,

    I think I figure out the issue, I found helpful explaining the HC not emit haplotypes, but try to best estimate the genotypes with high confidence. And you need extra steps to phase your sample, such as family information. As my understanding, haplotypeCaller will take advantage of the haplotype information for calling variants, but not necessary phasing the individual sample by default. Am I correct?

    Do you think it is a good explanation or I am off? The bam file is huge and I could not upload from my work.

    Sorry for the inconvenience.



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