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.

Joint genotyping of trio exome

I am running genotypeGVCFs for trio exome datasets (Father, Mother, and Child).

java -jar GenomeAnalysisTK.jar \
-T GenotypeGVCFs \
-R reference.fasta \
--variant father.g.vcf \
--variant mother.g.vcf \
--variant child.g.vcf \
-o output.vcf

I am wondering which variants are trio variants that are derived from father, mother, and child. How can I see from the vcf file? Could you please suggest me?

Example of result:

...
chr19 43355878 . G A 1088.92 . AC=3;AF=0.500;AN=6;BaseQRankSum=-3.460e-01;ClippingRankSum=0.00;DP=51;ExcessHet=3.0103;FS=1.358;MLEAC=3;MLEAF=0.500;MQ=41.72;MQRankSum=-2.136e+00;QD=13.44;ReadPosRankSum=-5.170e-01;SOR=0.952 GT:AD:DP:GQ:PGT:PID:PL 0/1:16,11:27:99:0|1:43355878_G_A:373,0,622
chr19 43355896 . G T 875.92 . AC=3;AF=0.500;AN=6;BaseQRankSum=0.569;ClippingRankSum=0.00;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=3;MLEAF=0.500;MQ=51.21;MQRankSum=-1.546e+00;QD=16.22;ReadPosRankSum=1.34;SOR=0.880 GT:AD:DP:GQ:PGT:PID:PL 0/1:11,7:18:99:0|1:43355878_G_A:302,0,425
...

Answers

Sign In or Register to comment.