How to Merge EIGENSTRAT Datasets Using mergeit

mergeit is part of the EIGENSOFT package and can be used to merge exactly two EIGENSTRAT/PACKEDANCESTRYMAP datasets without converting to PACKEDPED format first. In this post, I’ll show how to merge the sample we created in Pseudohaploid Genotyping for Ancient DNA: BAM to EIGENSTRAT with the AADR dataset.

Setting up EIGENSOFT

mergeit is part of the EIGENSOFT package. You can install it via conda:

conda install -c bioconda eigensoft

If you haven’t installed conda yet, see the Miniconda setup in the pseudohaploid genotyping post.

Alternatively, if you prefer to compile from source, see: From EIGENSTRAT to PACKEDPED.

Setting Up A Parameter File

Like other EIGENSOFT tools, mergeit requires a parameter file:

geno1: aadr.geno
snp1: aadr.snp
ind1: aadr.ind

geno2: eigenstrat_output.geno
snp2: eigenstrat_output.snp
ind2: eigenstrat_output.ind

genooutfilename: merged.geno
snpoutfilename: merged.snp
indoutfilename: merged.ind

Save this as mergeit.par and run:

mergeit -p mergeit.par

This produces merged.geno, merged.snp, and merged.ind, ready for downstream analysis with ADMIXTOOLS.