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

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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!


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