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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

GT:DP:GQ:MIN_DP:PL 0/0:150:0:150:0,0,0

Genotype of "GenotypeGVCFs"

Sample1 1/1:3,90:93:99:1|1:195452770_G_A:3389,144,0
Sample2 ./.:150,0:150
Sample3 0/1:71,42:113:99:0|1:195452770_G_A:1300,0,2473

"0/0" has been changed into "./."

Is this proper result?

Here is my command line.

"$(java) -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!!


  • SheilaSheila Broad InstituteMember, Broadie admin


    Notice the PLs are all 0 for that site. This is why the genotype has been set to ./. in the final VCF (the tool is not confident in any genotype).

    Can you please post IGV screenshots of the BAM file and bamout file in the region? Are you using the latest version of GATK?


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