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#CHROM characters allowed
I am trying to use GENOTYPE_GIVEN_ALLELES through HaplotypeCaller and have never run into this problem before. Everything is running as I expect, however I am really not getting any results even when it has parced through the alleles file past a variant position when it would typically be writing to a file as it goes. I am suspecting perhaps this is a problem within the chromosome names as I'm dealing with a file that both ";" and "=" were initially included in contig names by a collaborator. I changed out the = to an underscore because of issues caused previously, but now I am suspecting that perhaps the ";" semicolon is causing problems in GATK even though in VCF4.2 format it appears any character asides from a ":" colon and whitespace should be okay. Can someone comment on this?
I am out of other thoughts rather than having to go back through reference, vcf files and bam files/indexes to fix this character problem.