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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 \
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