calcExpectedHets: Calculates expected number of heterozygous SNPs

In quevedor2/WadingPool: A toolkit for shallow/low-pass whole genome sequencing analysis

Description

Takes a dbSNP file that is converted into the .bed format by the setup_dbSNP.sh script and runs simulations to calculate the expected number of heterozygous SNPs in a single sample given a target coverage fitted to a Poisson distribution.

Usage

calcExpectedHets(dbsnp_file, coverage = c(1), max_cnt = 2)

Arguments

dbsnp_file	Path to dbSNP bed file (from setup_dbSNP.sh)
coverage	Target coverage(s) and lambda param of rpois()
max_cnt	Count to set all dbSNP at for max point (default=2)

Value

A matrix for the input coverages and the mean, mean^2 (for 2 samples overlapping), standard error heterozygous SNPs (Expected values) and the number of SNPs

quevedor2/WadingPool documentation built on Dec. 22, 2021, 10:59 a.m.