Estimate naive allele frequency

Tool Information

This tool provides a naive implementation of estimating allele frequency from amino acid calls.

Allele frequency is estimated in two ways: - Allele frequency by read count: within sample allele proportions are calculated using read counts and then the allele frequency is calculated as the average within sample allele frequency - Allele frequency by presence/absence: allele frequency is calculated as the count of a particular allele divided by the total number of alleles observed at a given position

Script Usage

Rscript scripts/estimate_allele_frequency_naive/estimate_allele_frequency_naive.R \
  --aa_calls data/example_amino_acid_calls.tsv \
  --method read_count_prop \
  --output allele_freqs.tsv