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Welcome to UPDio, Version 0.9

Introduction UPDio is designed to identify uniparental disomy in probands of trio VCF data.

This directory contains 2 files 
	1. README.txt
		This file
	2. UPDio.pl
		The main calling script
and, three child directories
	1. scripts
		This contains some helper scripts for UPDio to run
	2. pre_processing
		This shall serve as a location to prepare samples for analysis
	3. sample_data
		This contains a pre-processed exome trio ready to be run on UPDio

UPDio requires 3 input files: these are the single-sample VCF files corresponding to the proband, mom, and dad samples of a trio
UPDio also recommends including a file of CNV calls for the proband; this is recommended to limit false positives

At the command line, type 'perldoc UPDio.pl' to familiarize yourself with how to run UPDio, then return here.

Setup This program is written in Perl and R Please ensure that dependencies are installed before attempting to run UPDio; they are all required. Dependencies can be downloaded from CPAN and CRAN.

R Dependencies
	quantsmooth
	ggplot2
Perl Dependencies
	Statistics::R (0.31)
	Path::Class
	Vcf
	Iterator::Simple
	List::MoreUtils
	Math::Round
	Const::Fast
UPDio was tested using R version 2.14.1

Pre-processing UPDio requires two input file format requirements: 1. The VCF files must be sorted in numeric chromosome order: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X We include a sort-vcf script to generate vcfs sorted in this order 2. The VCF files must include homozygous reference (homREF) genotypes, i.e. "0/0" positions We include a add_hom_refs_to_sorted_vcfs.pl script that can add these positions Note that your VCFs may already include 0/0 positions, if so, you can skip this step.

The pre_processing directory contains instructions for how to prepare input files for UPDio
Included in this directory is a commands file 'commands_to_preprocess_files.sh' showing the commands used to sort and add homREF positions.

Running UPDio First try running UPDio on the example trio that is supplied before running it on your own trio data To do this, refer to the file in 'scripts/run_UPDio_example.sh' containing the command to run UPDio on the example trio When this script has completed you should be able to observe a UPD event in the output files.

Output Output is stored by default in a directory called 'output_dir' but you can specify your own output directory as an option to UPDio Output files suffixes 1. table a tabulation of informative genotypes by chromosome 2. events_list a print out of informative genotypes found in the proband 3. upd a list of significant UPD events found (these lines can be long; try less -S to read this file) bear in mind that CNVs often masquerade as UPD events 4. pngs the plot of UPD events 5. log a log file

Troubleshooting Q: I'm getting an error message that looks like this: "Can't locate Statistics::R in @INC (@INC contains: ...)" A: Your perl dependencies are not installed; install all dependencies before running UPDio

Q: I'm getting an error message that says "cannot find set method in Statistics::R" A: You are using an older version of Statistics::R, please upgrade to 0.31