Rumex meiotic drive

This repository contains scripts used in the project of identifying meiotic drive in Rumex using pooled sequencing.

There're three folders including scripts for different analysis, in each script there're helpful comments and usage.

• transcriptome (analyze transcriptome alignments)

  • get_freq.py : allele frequency quantification without mapping bias correction
  • get_freq_nobias.py : allele frequency quantification with mapping bias correction

• genome (analyze genome alignments)

  • filt_vcf_pool1.py : filter and extract allele depths in pool 1 from VCF
  • freq_window.py : allele frequency quantification in sliding windows without mapping bias correction
  • freq_window_nobias.py : allele frequency quantification in sliding windows with mapping bias correction (still revising the bias correction formula)

• AF_DP (plot the average allele frequency at different depths)

  • get_freq_depth.py : get allele frequency and the depth at each informative site
  • get_depth_data.py : calculate the average allele frequency at different depths