Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
How to get exact allele frequency using HaplotypeCaller-GATK4 and speed up the running?
I have performed HaplotypeCaller in GATK4 (version:22.214.171.124) 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.