This file shows how to set customized genotyping parameters externally in a JSON file.
External genotyping parameter can be passed to multigrmpy.py and grmpy as JSON file with command line option -G
Below we show all allowed parameter fields:
{
// ploidy of samples
"ploidy": 2
// Minimal overlapping bases between a read and a mapped edge.
// Used in estimating distribution parameter in genotyper
"min_overlap_bases": 16,
// Minimal depth p value for a breakpoint to pass depth test
// a negative value disables this test, but you can use a value
// such as 0.00001 for a more conservative callset which only
// includes genotypes for calls which have read counts that are
// close to the median read depth in the BAM file.
"coverage_test_cutoff": 0.0001,
// Allele names in graph(s).
// If other alleles were observed in graph, they will be excluded from analysis.
"allele_names": [
"REF",
"ALT"
],
// Error rate for each allele.
// Alleles must be in the same orrder as "allele_names"
"allele_error_rates": [
0.04,
0.04
],
// These two fields will be effective only if "allele_error_rates" doesn't exist.
"reference_allele_error_rate": 0.05, // error rate of reference allele
"other_allele_error_rate": 0.05, // uniformed error rate of all alternative alleles
// Fraction of the non-reference allele in a reference-alternative heterozygotes.
// Alleles must be in the same order as "allele_names"
"het_haplotype_fractions": [
0.5,
0.45
],
// het_haplotype_fraction can be a float to represent a uniform fraction, such as:
// "het_haplotype_fractions": 0.5
// Fraction of each genotype in the population.
// Genotype indices are zero-based, relative to the "allele_names" array
"genotype_fractions": {
"0/0": 0.5,
"0/1": 0.3,
"1/1": 0.2
},
// This field will be effective only if "genotype_fractions" doesn't exist
"other_genotype_fraction": 0.33, // uniform genotype fraction for each genotype
}