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How to get exact allele frequency using HaplotypeCaller-GATK4 and speed up the running?
I have performed HaplotypeCaller in GATK4 (version:184.108.40.206) 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.