region or rs list rgPedSub.py $script_file No filter on relatedness - all subjects passed through Founders only (pedigree mother and father ID = "0") Offspring only (one randomly chosen if >1 sibs in family) Cut and paste a list of marker ids as rs numbers Supply genomic coordinates for a region (as UCSC location) title~~~~$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.