ustacks_setup: batch setup ustacks This function creates a bash job file for...

In JeffWeinell/misc.wrappers: Miscellaneous Wrapper Functions for Spatial Population Genomics

batch setup ustacks This function creates a bash job file for each combination of input sequence read files (one per individual), values of m and M to run STACKS. The output of this function is a character string vector with paths to bash job files, which can be piped to the function 'rsbatch' to submit the jobs.

Description

batch setup ustacks

This function creates a bash job file for each combination of input sequence read files (one per individual), values of m and M to run STACKS. The output of this function is a character string vector with paths to bash job files, which can be piped to the function 'rsbatch' to submit the jobs.

Usage

ustacks_setup(
  files,
  save.in,
  mMN = cbind(m = rep(3, 8), M = 1:8, N = 3:10),
  p = 16,
  ustacks.path = NULL
)

Arguments

files	Input sequence data files, one for each individual.
save.in	Character string with directory where output directories and files should be saved.
mMN	Three-column data frame or matrix with m, M, and N values in the first, second, and third columns, respectively. Each row indicates a combination of m, M, and N to use for STACKS. Default cbind(m=rep(3,8),M=1:8,N=3:10). m = Minimum depth of coverage required to create a stack. Default 3. M = Maximum distance (in nucleotides) allowed between stacks. Default 1-8. N = Maximum distance allowed to align secondary reads to primary stacks. Default 'M+2'.
p	Number of threads to use for job parallization. Default 16.
ustacks.path	Character string with path to the ustacks executable. Default NULL, in which case the path is derived from the default setting, which can be set with config_miscwrappers('<path/to/ustacks>').
N	Maximum distance allowed to align secondary reads to primary stacks. Default 'M+2'.

Value

Character string vector with the paths to bash job files.

JeffWeinell/misc.wrappers documentation built on Sept. 20, 2023, 12:42 p.m.