The purpose of this package ("snip-er") is to select variant frequency and sequence read depth thresholds to distinguish valid biological SNPs from sequencing/random error. Simulates how the genetic diversity (as measured by Shannon Diversity, Nucleotide (pi) Diversity, and Alternate Allele Frequency) per genomic site in an alignment of short reads is affected by altering sequence read depth or allele frequency.
User input: distribution of nucleotide frequencies at one genomic site (A, C, G, T) and number of replicate samples at each read depth.
Sample output:
