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Genotype "./." with depth 150 - GenotypeGVCFs
Hello GATK Team,
I have a question regarding GATK "GenotypeGVCFs".
I found some variants showed genotype "./." with resonable read depth from result file from "GenotypeGVCFs".
Genotype of sample1.g.vcf, sample2.g.vcf, sample3.g.vcf
Genotype of "GenotypeGVCFs"
"0/0" has been changed into "./."
Is this proper result?
Here is my command line.
"$(java) -Djava.io.tmpdir=/tmp -jar GenomeAnalysisTK.jar -T GenotypeGVCFs -R ucsc.hg19.fasta --variant multicall.gvcf.list --out ./rawVariants.vcf -L kit.bed --interval_padding 100 --disable_auto_index_creation_and_locking_when_reading_rods -nt 4"
Raw GVCF - "sample2.g.vcf"
chr3 195452799 . C . . END=195452799 GT:DP:GQ:MIN_DP:PL 0/0:150:0:150:0,0,0
Raw Result of "GenotypeGVCFs"
chr3 195452799 . C T 4659.89 PASS AC=3;AF=0.750;AN=4;BaseQRankSum=0.573;ClippingRankSum=0.039;DP=356;FS=4.543;MLEAC=3;MLEAF=0.750;MQ=47.26;MQRankSum=2.69;QD=22.62;ReadPosRankSum=1.12;SOR=1.030;set=variant GT:AD:DP:GQ:PGT:PID:PL 1/1:3,90:93:99:1|1:195452770_G_A:3389,144,0 ./.:150,0:150 0/1:71,42:113:99:0|1:195452770_G_A:1300,0,2473
To figure out the version problem, so I changed GATK 3.4 to GATK 3.6 but, I got same result - genotype "./." with DP 150.
Raw Result of "GenotypeGVCFs" - with GATK_3.6
chr3 195452799 . C T 4659.89 . AC=3;AF=0.750;AN=4;BaseQRankSum=0.597;ClippingRankSum=-7.070e-01;DP=356;ExcessHet=3.0103;FS=4.543;MLEAC=3;MLEAF=0.750;MQ=47.26;MQRankSum=2.69;QD=22.62;ReadPosRankSum=1.27;SOR=1.030 GT:AD:DP:GQ:PGT:PID:PL 1/1:3,90:93:99:1|1:195452770_G_A:3389,144,0 ./.:150,0:150:.:.:.:0,0,0
Thank you in advance!!