A study of the evolutionary mutational signatures inferred through the gVCF files and FASTA files resourced from the Zoonomia Project
For each generation, is estimated that 100-200 new mutations enter the DNA, a process that together with recombination is thought to push evolution forward. In this research, we analyzed the genetic data provided by the Zoonomia Consortium and deconvoluted evolutionary mutational signatures: a representation of mutational patterns over many generations of evolution of 119 eutherian mammalian species. A pipeline to calculate these signatures and deconvolute them has been built, hoping to shed light on similar mutational processes occurring in humans, and in human cancer cells.
Due to uncertainty in the variant calling, the exact direction of the mutations is unknown ( e.g. A->C or C->A), so the results are are not informative in the form of a 96-entry vector, but just as a 48-entry vector.
CONTENT OF THE REPOSITORY
-exporting.sh : To extract a fasta file from the HAL file
-sort_scaffolds.sh : To sort the scaffolds in the FASTA files and order them by scaffold number
-fasta_TO_gav.sh : To eliminate the new line tab between scaffold number and DNA sequence
-Signature1.R : To read gVCF file and a modified FASTA file, and to build the mutational histogram
-graph.R : To make the graph of the signature once the histogram has been calculated
-graph2.R : To make a "compressed" mutational signature, a 6-entry histogram where we do not account for the nearest neighbors of the mutated nucleotides
-test_nmf.R : To read all the output files generated by "Signature1.R", build a matrix with all the mutational histograms, and prepare for deconvolution; to test the possible number of signatures to deconvolute, and then use nmf to do so. It also generates many graphs, depicts the deconvoluted signatures, and compares them with the ones in the COSMIC database (generated from human cancer samples)
-41586_2020_2876_MOESM3_ESM.csv : The list of species that were analyzed by the Zoonomia consortium
-"outfile_AcoCah.txt", "acocah.jpeg" and "acocah1.jpeg" are examnple of the outputs of "Sigature1.R", "graph.R" and "graph2.R" respectively, for the specie Acomys Cahirinus
DATA AVAILABILITY
gVCF files: https://data.broadinstitute.org/200m_variation/
HAL library: https://github.com/ComparativeGenomicsToolkit/hal