Haplotype Caller: too many alternative alleles found?
Hello gatk team,
I am running HaplotypeCaller on 5 files of genomic alignments together at once.
Despite the fact that I did a InDel realignment (Indel Realigner gatk) before running these files with HaplotypeCaller, I get many warnings during the process that say "too many alternative alleles found", with sometimes 10, 12 or 13 alternative alleles found.
Is that normal? or is there a step that I could have done improperly?
Thank you for your help