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How to get exact allele frequency using HaplotypeCaller-GATK4 and speed up the running?

YenanYenan Member
edited October 2018 in Ask the GATK team

Hi there,

I have performed HaplotypeCaller in GATK4 (version:4.0.9.0) for variant calling of germline DNA. Here are the results in the vcf file.

chr1    17365   rs369606208 C   G   146.77  .   AC=1;**AF=0.500**;AN=2;BaseQRankSum=-1.215;DB;DP=53;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=40.27;MQRankSum=-0.719;QD=2.77;ReadPosRankSum=-0.581;SOR=0.664 **GT:AD:DP:GQ:PL    0/1:43,10:53:99:175,0,1354**
chr1    17407   rs372841554 G   A   249.77  .   AC=1;**AF=0.500**;AN=2;BaseQRankSum=-0.924;DB;DP=106;ExcessHet=3.0103;FS=2.034;MLEAC=1;MLEAF=0.500;MQ=46.70;MQRankSum=-0.797;QD=2.36;ReadPosRankSum=0.729;SOR=0.433 **GT:AD:DP:GQ:PL    0/1:84,22:106:99:278,0,2088**
chr1    981931  rs2465128   A   G   2859.77 .   AC=2;**AF=1.00**;AN=2;BaseQRankSum=0.989;DB;DP=98;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=29.18;ReadPosRankSum=-0.013;SOR=1.313    **GT:AD:DP:GQ:PL    1/1:2,96:98:99:2888,239,0**

As you can see, all the AF are the estimated 0.5 or 1.0, but not exact number. At the meantime, I ran the Mutect2-GATK4 for another sample, and I could get the exact AF from Mutect2. Would you please help me to figure this out?

Here is the script for HaplotypeCaller:

java-options "-Xmx40g" HaplotypeCaller \
-R /data3/IonProton/bwa-index_hg19/hg19_forGATK_sinica.fa \
-I 13029-10ng_F0x100_intersect.bam \
-O 13029-10ng_F0x100_intersect_HC.vcf.gz \
--dbsnp /data3/IonProton/bwa-index_hg19/dbsnp_138.hg19.vcf

In addition, is there any way to speed up the running of HaplotypeCaller and Mutect2? On single job(sample) of HaplotypeCaller and Mutect2 took me about 14hr and 19hr, respectively.

Thank you!

Post edited by shlee on

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