nitinra/PopGenCode

Various bits of code for population genetic methods used in my publications

PopGenCode

Various bits of code for population genetic methods used in my publications

Compute D_xy from site frequency spectrum

Code used to compute D_xy in 10kb-windows across the genome in Marques et al. 2018 in press.

1) Estimate 2D-SFS in windows using angsd

I used the code in run10kdxy.pbs to compute 2D-SFS in predefined windows given in a BED-format file (e.g. file windows.chrI.GLA.10k.bed listing all 10kb-windows on chromosome I). For each line in the BED-file, the script runs angsd twice to generate a temporary SAF file for the specific window for both populations (defined by bam file lists) and then runs realSFS, which computes the 2D-SFS. Chromsome, start and end position of the window and the realSFS output are then added to the outfile, one line per line (see file example.10kwin.sfs). Sorry for the hard-coded format...

2) Compute D_xy from 2D-SFS file

Once you have a file generated by the above script with chromosome, start, end position and SFS entries (file example.10kwin.sfs), the script dxy_wsfs.py computes D_xy for each line in the file.