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GenotypeGVCF: skipped sites

Dear devs,
I'm working on GATK v.3.7 in order to genotype more than 700 samples.
Before using GenotypeGVCFs, I used CombineGVCFs. GenotypeGVCFs works fine, but I'm looking for a solution about this warning message:

WARN 15:20:11,636 GenotypingEngine - Attempting to genotype more than 50 alleles. Site will be skipped at location chr2:179510831

I tried to modify --max_alternate_alleles option but it doesn't work. I also modified --max_genotype_count option, but GATK doesn't recognize this option and I got this error (I didn't find this option in --help message):

ERROR MESSAGE: Argument with name 'max_genotype_count' isn't defined.

Looking at that sites, it seems to be an highly variable site but most of those variants are true positive. Is there any way to avoid this error and to get all genotypes for that position?

Thank you for your time,

Best Answer


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