Tail-Loss-Primates

This repository contains scripts used for identifying hominoid-specific variants in genes related to tail development.

Overview

01_identify_mutations

In order to identify variants associated with the tail loss phenotype, we conducted a comparative phylogenetic study to scan for hominoid-specific variants in 140 genes (+/-10kb) related to tail development. The full gene list is attached in file gene140_location.csv (adapted from Ensembl BIOMART). Tbxt gene is used as an example for the pipeline.
Taking Tbxt gene as an example:
First extract the multiple sequence alignments for each gene. Whole genome alignment can be downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz30way/. Eight sequences including six hominoid species ("hg38", "gorGor5", "panTro5", "panPan2", "ponAbe2", "nomLeu3") and two non-hominoid species("macNem1","calJac3") are extracted. Example output is TBXT_new_8species.fasta

Rscript 140gene_fasta_new_8species.R "$chromosomeID"  

Then hominoid-specific variants can be identified by

python mutation.py TBXT_new_8species.fasta   

For 140 genes, after gathering fasta file for each gene, run:

bash forloop_python.sh

02_classify_mutations

inputs/ contain 140 csv files generated from step 1 (identify mutations). For each of the 140 genes, variants are classified into insertions, deletions and SNPs. Each type of variant is stored as a bed file in the outputs/.

Rscript mutation_classifier.R

03_predict_via_vep

First concatenate all the SNPs, deletions and insertions among 140 genes

cat 02_classify_mutations/*_snp.bed > total_snp.bed  
cat 02_classify_mutations/*_deletion.bed > total_del.bed  
cat 02_classify_mutations/*_insertion.bed > total_ins.bed

Outputs are saved in 03_predict_via_vep/.

04_filter_vep_results

Rscript filter_vep_visualization.R

Output files and plot are stored in 04_filter_vep_results/