I have estimated genome-wide heterozygosity levels using maximum likelihood and classical substitution model implemented in package atlas. These estimates are way more robust than classical SNP calling and simply counting number of heterogeneous locations because they integrate information from a big window into one estimate. I.e. I am quite sure about heterozygosity levels of SNPs of my genomes.
However, now I would like to know also about heterozygosity of indels and call individual snps using my robust estimates as a prior. GATK allows to specify priors on heterozygosity both of SNPs and indels, which might improve variant calls a lot, because default GATK is parametrised for human (Default priors for heterozygous SNPs is 0.001 and for indel 1.25E-4.). But, I work with insects I know that my SNPs heterozygosity is somewhere between 0.01 and 0.03 (1% - 3%).
So here comes the question, if I know the heterozygosity of SNPs, can I simply guess a reasonable prior for the heterozygosity of indels? GATK defaults for priors are 10x different, should I assume the same relation? Is there a reasonable way how to guess a prior for heterozygosity of indels?