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MultiEigenMerge

The original program for merging genotype files in eigenstrat format, i.e., mergeit.c enclosed in EIGENSOFT (https://github.com/DReichLab/EIG) and ADMIXTOOLS (https://github.com/DReichLab/AdmixTools) packages, can only merge two files every time. Accounting that, I wrote this R code MultiEigenMerge.R to generate parameter files and the bash file for merging multiple (>2) genotype files in eigenstrat format.

INPUT

  • merged.file.list.DIR: a list containing the prefixes of all the eigenstrat files you want to merge - one line per prefix. E.g., v50.0_1240K_public is the prefix of v50.0_1240K_public.geno, v50.0_1240K_public.snp, and v50.0_1240K_public.ind.
  • fixed.par.file.DIR: the part of parameter file that does not change, i.e, except for the name of input and output eigenstrat files.
  • mergeit.DIR: the directory of compiled mergeit program.

OUTPUT

  • output.file.prefix: the prefix of newly generated eigenstrat file.
  • do_mergeit.sh: the bash file used for running mergeit.