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CombineVariants results in completely wrong genotype fields in multithreaded mode; a bug?
Dear GATK team,
I spotted this behavior a while ago (I think in the pre-release, beta version) and unfortunately thought it would be fixed. But it still seems to be there.
When you combine 2 vcf files with CombineVariants in a multithreaded mode for some variants it produces totally wrong numbers in the AD,DP,GQ fields.
Way off from real numbers in initial vcfs, sometimes going into thousands instead of tens!
It works correctly in single thread mode...
It seems there is a serious bug somewhere. Not all variants are affected, but you can do diff on two files made with 1 thread and multiple thread mode.