aggregateAndFilter: Aggregate samples and filter SNPs

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

Description

Works in conjunction with the genSnpZygosity() function. This function will take the output from that function and concatenate each samples SNP results into a csv. It will then go through each SNP to identify whether X or more samples have coverage on that SNP and isolate the genomic location and genotypes for those SNPs

Usage

aggregateAndFilter(
  s_paths,
  dbsnp_dir,
  num_samples = 2,
  dbsnp_file = "all.common_all_20151104.bed",
  chrs = paste0("chr", c(1:22, "X", "Y"))
)

Arguments

s_paths	Sample SNP paths from genSnpZygosity()
dbsnp_dir	Directory containing the chr-dbSNP bed files
num_samples	Number of samples required to have that SNP [Default=2]
dbsnp_file	Main dbSNP file before splitting [default=all.common_all_20151104.bed]
chrs	List of chrs [Default=chr1, chr2, .., chrY]

Value

A vector of the input, output files and runtime

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