/Neurospora_mutation

Mutation analyses in Neurospora genome

Primary LanguagePerl

Scripts and pipelines for mutation analyses in Neurspora crassa

Folders

Correlations

  • R scripts for analysis of relationships between predictor variables and mutation rate across taxa (contributed by Laurence D. Hurst)

Dup-Period

  • Perl scripts to search for interspersed homology (contributed by Huawei Tan)

Simulation

  • Perl scripts for mutation simulation (i.e., generating synthetic mutations)
  • An example from preprocessing to mutation calling could be found in Simulation Step 4~6

Spontaneous_Dup

  • Steps to detect spontaneous duplicates using Delly

Scripts

detect_tetrad_mutations.pl

Detect mutations in parent-tetrad/ascus samples

  • Usage:

      detect_tetrad_mutations.pl -v variants.vcf -g sample_groups.txt --min-supp-depth 5 mut.vcf

  • Options:

      -v, --vcf     <filename>
      input vcf file, required
      
  Note: This script is designed to process vcf files with AD (Allele Depth) field for each sample
   
  -o, --output  <filename>
      output filename, default to STDOUT
  
  -q, --quality     <float>
      loci with quality smaller than this value will filtered
  
  
  -g, --group-file  <file>
      file contain group infos of each sample, each sample per line, e.g.
      sample1 group1
      sample2 group1
      sample3 group2
      ...
      set this option to screen group-specific mutation, only samples belong
      to different groups would be used as compare samples
      
  
  --min-supp-depth  <int>
      minimum number of supporting reads, for multiple samples carry the same
      mutation, only one need to pass this criterion [default: 1]