cpSNPsVCF: copy STACKS SNPs VCF files using informative names Copies...

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

copy STACKS SNPs VCF files using informative names Copies each of the 'populations.snps.vcf' files generated by the 'populations' program of the STACKS pipeline, and uses a more informative filename. This function will only work if the 'populations_setup' function was used for running populations.

Description

copy STACKS SNPs VCF files using informative names

Copies each of the 'populations.snps.vcf' files generated by the 'populations' program of the STACKS pipeline, and uses a more informative filename. This function will only work if the 'populations_setup' function was used for running populations.

Usage

cpSNPsVCF(indir, outdir, groupname = NULL)

Arguments

indir	Character string with the parent directory where STACKS output files and directories are held for a particular group.
outdir	Character string with path to directory where 'populations.snps.vcf' files should be copied. These will be renamed with the groupname stacks parameters.
groupname	Character string with name of the group (usually a taxon). Default is NULL, in which case the groupname is the directory name supplied by indir,i.e., the result of basename(indir).

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