To enrich the variant query command line, we should to provide new parameters in order to allow users to filter by the minor allele frequency (maf), the minor genotype frequency (mgf), the number of missing alleles or genotypes... for a given study and cohort.
Some example of these parameter should be:
--maf for the minor allele frequency
--mgf for the minor genotype frequency
--missing-allele for the number of missing alleles
--missing-genotype for the number of missing genotypes
The expected value for these parameters should be (and enclosed with double quotes):
study_name:population_name[<|>|<=|>=|==|!=]numeric_value
For instance:
--maf "1000g:all<0.25" --mgf "1000g:all<=0.5" --missing-allele "1000g:all==5" --missing-allele "1000g:all!=0"
To enrich the variant query command line, we should to provide new parameters in order to allow users to filter by the minor allele frequency (maf), the minor genotype frequency (mgf), the number of missing alleles or genotypes... for a given study and cohort.
Some example of these parameter should be: --maf for the minor allele frequency --mgf for the minor genotype frequency --missing-allele for the number of missing alleles --missing-genotype for the number of missing genotypes
The expected value for these parameters should be (and enclosed with double quotes): study_name:population_name[<|>|<=|>=|==|!=]numeric_value
For instance: --maf "1000g:all<0.25" --mgf "1000g:all<=0.5" --missing-allele "1000g:all==5" --missing-allele "1000g:all!=0"