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105 changes: 54 additions & 51 deletions version_1.0/README.md
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Expand Up @@ -2,35 +2,36 @@ Welcome to UPDio, Version 1.0

# This verison adds mulitsample support.

Introduction
UPDio is designed to identify uniparental disomy in probands of trio VCF data.
## 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
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 requires 3 input files: these are the single-sample VCF files corresponding to the proband, mom, and dad samples of a trio
# update: or one (child mother father) trio multisample VCF file.

UPDio also recommends including a file of CNV calls for the proband; this is recommended to limit false positives
UPDio also recommends including a file of CNV calls for the proband; this is recommended to limit false positives
# this step is especially important when detecting smaller UPD events

At the command line, type 'perldoc UPDio.pl' to familiarize yourself with how to run UPDio, then return here.
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.
## 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
Expand All @@ -45,46 +46,48 @@ Setup
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
## 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
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.
# If this doesn't work, email me and I'll make the positions file for you.
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.
# If this doesn't work, email me and I'll make the positions file for you.
# SureSelect_v4 is now on github, SureSelect_v5 soon to be uploaded

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.
## 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
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
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: ...)"
## 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"
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

Q: How can I gain access to 1000 MAFs to select common sites in my exome design?
Q: How can I gain access to 1000 MAFs to select common sites in my exome design?
A: Sorry, this file was too large to load to github! Solutions: https://www.biostars.org/p/6897/ or email me.