mastersproject

This repository is part of my master's project at Univerity of Geneva. It contains multiple scripts used during the project. If you have any questions, please contact adriano.weber@etu.unige.ch

The main features are:

• load_phased1KGP.sh: A shell script to dowload high coverage data from the 1000 genomes project(1KGP) for the phased VCF files. This script allows selection of loci and continent.
• load_30x1KGP.sh: A shell script to dowload high coverage data from the 1000 genomes project(1KGP) from NYGC_GATK. This script allows selection of loci and continent.
• load_release31KGP.sh: A shell script to dowload data from the 1000 genomes project(1KGP) for the phase3 release of variant calls. This script allows selection of loci and continent.
• vcf2uniformat.sh: A shell script to transform a VCF file into UNIFORMAT style. This script is designed to get inpute files for the Gene[rate] tool. Beware if adapting the script, since it depends on the length of haplotypes.
• handlingmisdata.sh: A shell script completing missing data due to multi-samples vcf merging. It must have bam files to query the coverage depth of every missing data with samtools depth.
• star_allele_info.sh: A shell script that select star allele SNPs for a gene in a VCF file and compute the frequency of this allele in a population (MUS by default). Beware if adapting the script, it is made for a population named "MUS".
• plot_plinkpca.R: A R script to plot the output of a PLINK pca.
• rsID.sh: A shell script to annotate VCF files with rsID (secondary so still not fully implemented).