Seems VariantsToTable not properly handle AD greater than 100
closed | Created 2019-08-23 | Last updated 2019-09-05| Posted by bshifaw | See in Github


Vanilla bug


User provided input files that i tested and one of the AD values did get concatenated but not all AD values greater than 100 were concatenated.

User post


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<br />
```<br />
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:<br />
```<br />
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<br />
```<br />
And here is the corresponding row in the tsv file:<br />
```<br />
CHROM   POS REF ALT QUAL    S1.AD   S1.GQ   S1.PL   S1.GT   S2.AD   S2.GQ   S2.PL   S2.GT<br />
1   15880   G   A   3785.46 58,35   99  895,0,2296  G/A 98105   99  2900,0,3782 G/A<br />
```<br />
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.

This Issue was generated from your [forums] 
[forums]: https://gatkforums.broadinstitute.org/gatk/discussion/24368/seems-variantstotable-not-properly-handle-ad-greater-than-100/p1

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