ABBA-BABA

Inference of Hybridization and Introgression Events using ABBA-BABA (Figure 4)

Author: Michael Seidel

Basis for Figures and Tables

• Figure 4B
• Figure S12

Usage

The script angsd_sge.py is designed to be executed in a grid scheduling environment (like SGE). A command line for submission is presented upon execution. The script expects one mandatory parameter to choose the grouping by chromosome, subgenome or both.

Additional files are required by angsd, please refer to the documentation of ANGSD for more details. Samples for both files are included in this repository for your reference.

Input:

• bamfiles.list A list of all samples that should be included in the analysis
• sizeFile.size The number of lines in the bamfile that form one group, e.g. lines 1-5 are group A, lines 6-10 group B and lines 11-20 group C, then the sizes are 5, 5 and 10.

Output:

The angsd generates output files with extension:

• .result.Observed.txt D-statistic calculated WITHOUT Error Correction and WITHOUT Ancient Transition removal (from the ANGSD website)

• .result.TransRem.txt D-statistic calculated WITHOUT Error Correction and WITH Ancient Transition removal (from the ANGSD website). This output was used for the subsequent analyses.

Code:

1. angsd_sge.py

External software (beyond imported packages):

1. ANGSD