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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,