region or rs list
rgPedSub.py $script_file
title~~~~$title
output1~~~~$output1
userId~~~~$userId
outformat~~~~lped
basename~~~~$input1.metadata.base_name
inped~~~~$input1.extra_files_path/$input1.metadata.base_name
outdir~~~~$output1.files_path
relfilter~~~~$relfilter
#if $m.mtype=='grslist'
rslist~~~~$m.rslist
region~~~~
#else
rslist~~~~
region~~~~$m.region
#end if
.. class:: infomark
**Note**
There are 2 forms to complete before the job is ready to be run
**Page 1**
give the job a mnemonic descriptive title and select the output format.
Choose a file containing genotypes and a pedigree from your current history
The input file must be in linkage ped format.
If the data are not yet in your history, import from one of the system libraries or upload from your computer using the get data tool
**Page 2**
Define the markers to be used. You can supply a UCSC style location as chr:start_offset-end_offset
or a list of marker ids - rs numbers. You can flip between marker input style by changing the select box.
If you supply a list, the markers must all be from the same chromosome or region for sensible results.
Run the job and the subset file will eventually appear in your history ready to be used with other tools.
-----
**Syntax**
- **Library Linkage Ped** is a linkage format pedigree file chosen from the system file Library
- **History Linkage Ped** is a linkage format pedigree file chosen from your current Galaxy History
- **Region** is the genomic region cut and paste from a UCSC browser location window
- **Genome Build** is the version of the genome your markers are from - use hg18 for CAMP illumina data
-----
.. class:: infomark
**Summary**
This tool is a special purpose tool to extract genotypes from genotype data in linkage
pedigree format (separate map file) over a specified genomic region
The region to be extracted can be described as UCSC browser location, or as a list of
markers.
It is possible to retain ALL markers by leaving the rslist and region empty if you just want to remove
all offspring from a pedigree for example
The extracted data will appear in your current history as a new lped data set
Copyright, Ross Lazarus, March 2008 for the Rgenetics project
Released under the LGPL. See http://www.gnu.org/licenses/lgpl.html for license terms.