README
This is the repository for López EH & Palumbi SR (2020). Somatic mutations and genome stability maintenance in clonal coral colonies. Molecular Biology and Evolution 37:828-838 DOI: 10.1093/molbev/msz270

The following steps will take a VCF file with multiple genotyped samples and produce a list of putative somatic mutation sites, the genotypes at each putative site for each sample, and the characteristics of each putative mutation.

The steps shown here use colony AH09 as an example.

1. run VCFtodatatable.py

input file: AH09_Aug2011_cohort_20180106_merged_filtered_nomissing_nosym_noblanks.vcf
output file: AH09datatable20181029.txt

2. run AH75melted.R
input file: AH09datatable20181029.txt
output file: meltedAH09datatable20181029.txt

3. run definemutationtypes.py
input files: AH09datatable20181029.txt , Genotypes_trimmed.txt , meltedAH09datatable20181029.txt
output file: meltedAH09datatable_withtransitionandpopinfo.txt

4. do Sanger verifications, update your files accordingly.
output file: melted_AH09_datatable20181029_withtransitionandpopinfo_withverificationsFOR_R.txt

5. Analyses in R