i have been using HaplotypeCaller in gVCF mode on a cohort of 830 samples spread over 2450 bams. the number of bams per sample varies from 1-4. for samples with <=3 bams, the routine works perfectly. but for samples with 4 bams, the jobs always crash and I receive the error:
ERROR MESSAGE: Invalid command line: Argument emitRefConfidence has a bad value: Can only be used in single sample mode currently
is this a bug? are there any options i can use to avoid this error. i suppose it is possible that there is an issue with my bams, but it seems odd that the error occurs systematically with 4 bam samples and never for samples with 3 or fewer bams.
thanks for any help!