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Maximum number of files with GATK CombineVariants ?

ekofmanekofman Member, Broadie

We are trying to merge 8614 VCF files using CombineVariants and it's failing with this error on file ~4020ish of our list of 8614.

Error:
ERROR MESSAGE: Unable to create BasicFeatureReader using feature file , for input source: /xchip/

Is there a limit to the number of files mergeable with this tool? Can we get around this?

Answers

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