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Seems VariantsToTable not properly handle AD greater than 100

jzhangjzhang North Carolina, USAMember
edited August 21 in Ask the GATK team
I am trying to extract info from a vcf file using the following command and encountered a problem:
```
gatk VariantsToTable -R $REF -V final_SNP.vcf -F CHROM -F POS -F REF -F ALT -F QUAL -GF AD -GF GQ -GF PL -GF GT -O snpPE_final.tsv
```
For SNPs with its AD value less than 100, the results are fine, but for SNPs with its AD value greater than 100, VariantsToTable just concatenates the two AD values. Here is an entry in the vcf file:
```
1 15880 . G A 3785.46 PASS AC=2;AF=0.500;AN=4;BaseQRankSum=6.325;DP=296;ExcessHet=4.7712;FS=3.153;MLEAC=2;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=12.79;ReadPosRankSum=-1.165;SOR=0.888 GT:AD:DP:GQ:PL 0/1:58,35:93:99:895,0,2296 0/1:98,105:203:99:2900,0,3782
```
And here is the corresponding row in the tsv file:
```
CHROM POS REF ALT QUAL S1.AD S1.GQ S1.PL S1.GT S2.AD S2.GQ S2.PL S2.GT
1 15880 G A 3785.46 58,35 99 895,0,2296 G/A 98105 99 2900,0,3782 G/A
```
The AD values in the S2.AD column should be 98,105, not 98105. I use GATK4-4.1.2.0-1 and openjdk 1.8.0_152-release on Ubuntu 18.04.
Post edited by jzhang on

Issue · Github
by bshifaw

Issue Number
6115
State
open
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