Tagged with #prioritize
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Hi,

I'm just reverse engineering a colleagues script and I've noticed they're using CombineVariants in PRIORITIZE mode but without a -priority argument. I've looked at the documentation and I can't see what the defined behaviour would be in this situation. Would default priority in this situation follow the order of the arguments supplied; the reverse order; or random?

Thanks, Martin

Edit: Nevermind, from what I can see from the source it should be erroring out if -priority is not supplied. I must have missed something in the pipeline script.

Edit 2: No wait

    if ( genotypeMergeOption == VariantContextUtils.GenotypeMergeType.PRIORITIZE && PRIORITY_STRING == null )
        throw new UserException.MissingArgument("rod_priority_list", "Priority string must be provided if you want to prioritize genotypes");

is pointless because this is run first in initialize:

    if ( PRIORITY_STRING == null ) {
        PRIORITY_STRING = Utils.join(",", vcfRods.keySet());
        logger.info("Priority string not provided, using arbitrary genotyping order: " + PRIORITY_STRING);
    }

This should follow the input order yes? Unless vcfRods.keySet is sorted?