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maxAltAlleles in GenotypeGVCFs
We have used the 3.x workflow to process targeted resequencing for a large cohort. At the genotypeGVCFs stage, we get the following warning in the output:
ExactAFCalc - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at chr:pos has NN alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
Since our cohort is very large, it is extremely unlikely, but not impossible that more than 6 indel alleles exist at a given locus. Accordingly, allowing genotypeGVCFs to consider more possible alleles seems warranted.
While --max_alternate_alleles is an option for HaplotypeCaller, it is not recognized by genotypeGVCFs. Is this parameter fixed for genotypeGVCFs? If not, is there a way to change this parameter at the genotypeGVCFs stage? If not, can this parameter be modified by altering the combined GVCF header or rerunning HaplotypeCaller with a higher value for --max_alternate_alleles?
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