diff --git a/version_1.0/README.md b/version_1.0/README.md index d57dfc9..89eea04 100755 --- a/version_1.0/README.md +++ b/version_1.0/README.md @@ -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 @@ -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.