bella2347 / git-exjobb

Git repository for my degree project in Molecular Biotechnology Engineering at the Department of Ecology and Genetics, evolutionary biology.

Git repository for degree project in Molecular Biotechnology Engineering at the Department of Ecology and Genetics, evolutionary biology.

chr_mapping_contigs.py : was used to extract the scaffolds that map to chromosomes extract_individuals.py : was used to extract individuals specified in a file remove_P.py : was used to remove the position row in fastPHASE input-files, the position row is saved as a separate file to be used in LDhelmet split_lines.py : used to split fastPHASE input that have to many characters on each line ldhelmet_inp.py : was used to create LDhelmet input-files from fastPHASE v1.4 output, can take a file of samples and only include them ancestral_from_vcf.py : was used to test if at least two of three groups are monomorphic for the same allele prior_prob_state.py : create the ancestral files used in LDhelmet from the output from the ancestral_from_vcf.py script

The files for the analysis with R were used to get the means and other results. The ones in the directory analysis_local were used locally on my computer and can not be used as they are but shows how correlation coefficients were found and plots were made.

not_used_scripts : not used in the final project

countMissing.py : not used in the final project, counts the number of missing genotypes at each position from fastPHASE input-files