The current GATK version is 3.2-2

#### Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Bug Bulletin: The recent 3.2 release fixes many issues. If you run into a problem, please try the latest version before posting a bug report, as your problem may already have been solved.

# -T CombineVariants ##### ERROR MESSAGE: For input string: "20"

Posts: 3Member
edited January 2013

Hello,

I called variants in chunks (100000 bp chunks) on chromosome 20 on 450 reduced BAMS using -T UnifiedGenotyper, which resulted in the generation of 631 VCFs.

Now I want to combine these 631 VCFs using -T CombineVariants, however there seems to be a problem with some of the VCFs and all I get is an error message.

I can combine the 5 first VCFs that were generated, but when I add a sixth one (chr20:400000_500000) I get the following error:

##### ERROR MESSAGE: For input string: "20"

If I exclude that file, I can combine about 30 VCFs until I encounter a similar error message for a different VCF file:

##### ERROR MESSAGE: For input string: "120"

I've looked through both of the "problematic" VCFs and can't see how they differ from the ones that I can combine.

Any idea of what may be going wrong and how I can solve this? At the moment I can only identify problematic VCF by trying to combine them using CombineVariants since I don't know what it is about these particular VCF files that is causing the problem.

Thanks for your help, Tota

Post edited by Geraldine_VdAuwera on
Tagged:

Hi Tota,

Can you tell me what version of GATK you're using? Also, can you post the full error message with stack trace?

Geraldine Van der Auwera, PhD

• Posts: 3Member

Hi Geraldine,

Im using GATK v2.1-11-g13c0244 and this command (for 2 VCFs, where chr20_400000_500000.vcf is the problematic one):

java -jar gatk-2.1-11/GenomeAnalysisTK.jar -R hs37d5.fa --variant chr20_300000_400000.vcf --variant chr20_400000_500000.vcf -o combined.var.vcf -T CombineVariants

and here is the ERROR message: