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How can I use CombineVariants with Queue
Queue is unable to build a proper job graph if I do something like this:
combineVariants.variant +:= gtHaplotypeCaller.out + ":HC" combineVariants.variant +:= gtUnifiedGenotyperSNP.out + ":UGSNP" combineVariants.variant +:= gtUnifiedGenotyperINDEL.out + ":UGINDEL" combineVariants.genotypeMergeOptions = GATKVariantContextUtils.GenotypeMergeType.PRIORITIZE combineVariants.priority = "HC,UGSNP.UGINDEL"
The problem seems to be by not using exactly the output values from the other jobs, Queue is unable to properly link output from required jobs before CombineVariants.
I also tried:
combineVariants.variant +:= gtHaplotypeCaller.out combineVariants.variant +:= gtUnifiedGenotyperSNP.out combineVariants.variant +:= gtUnifiedGenotyperINDEL.out combineVariants.genotypeMergeOptions = GATKVariantContextUtils.GenotypeMergeType.PRIORITIZE combineVariants.priority = "variants,variants2,variants3"
In this case I get:
##### ERROR MESSAGE: Invalid command line: Argument rod_priority_list has a bad value: Not all priority elements provided as input RODs: variants,variants2,variants3
Any recommendation on how to run CombineVariants using Queue and merge type