GeneratingSimpleRecombinationMap

• 1 Introduction
• 2 Requirements
• 3 Run the script

1 Introduction

As input MimicrEE2 uses a recombination map (optional parameter; per default no recombination is used).
We provide a script that generates a simple recombination map for a given MimicrEE2 haplotype file.

2 Requirements

• Download the haplotypes (from the Drosophila Genetic Reference Panel): https://sourceforge.net/projects/mimicree2/files/starvation_resistance/mimicree_format_dgrp_snps_X_chromosome.gz/download
• Download the script https://sourceforge.net/projects/mimicree2/files/scripts/simple-recombination-map.py/download

3 Run the script

The following script generates a recombination map for each chromosome in the MimicrEE2 haplotype file. It will use the provided recombination rate in centiMorgan per megabasepair for each chromosome.

python simple-recombination-map.py --mimhap mimicree_format_dgrp_snps_X_chromosome.gz --rr 4 > rr.txt

This yields:

[cM/Mb]
2L:1..23011266  4
3R:1..27898798  4
X:1..22422335   4
2R:1..21146319  4
3L:1..24535547  4

This file can now be used in simulations with MimicrEE2, for example using the command:

java -jar mim2.jar w --recombination-rate rr.txt --haplotypes-g0 mimicree_format_dgrp_snps_X_chromosome.gz --snapshots 10 --replicate-runs 1 --output-sync rr-test.sync