and comparisons with HapMap data rgHaploView.py "$ucsc_region" "$rslist" "$title" "$out_file1" "$lhistIn.extra_files_path" "$lhistIn.metadata.base_name" "$minmaf" "$maxdist" "$ldtype" "$hires" "$memsize" "$out_file1.files_path" "$infoTrack" "$tagr2" "$hmpanel" ${GALAXY_DATA_INDEX_DIR}/shared/jars/haploview.jar rsquared (default) D prime D prime alternative Gabriel 4 Gamete test CEPH (European) (default) Yoruba (African) Chinese + Japanese (None - no comparison) Add Information track (DISABLED! Awaiting fix from Haploview authors) No Information track High resolution - only a few (hundreds of) markers Low resolution - large number of markers 1GB 2GB (default) 4GB 6GB 8GB

.. class:: infomark **Note** The input file must be in linkage ped format. A suitable file can be chosen from the system library, or from the files already imported into your current history. Use either one of the selection boxes to make your choice. ----- **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 ----- **Summary** This tool is a special purpose tool to estimate and plot linkage disequilibrium estimated from genotype data in linkage pedigree format (separate map file). All markers in the input file are used as the default. To limit the calculations to a subset of the input data, supply a specified genomic region in UCSC browser location format or a list of specific marker IDs. Note that you can choose either a file of the correct type (linkage pedigree - lped) from your current history **or** from the system library This tool currently calls Haploview for estimation and plots. For full attribution, source code and documentation, see http://www.broad.mit.edu/mpg/haploview/index.php Copyright, Ross Lazarus, April 2008 for the Rgenetics project Released under the LGPL. See http://www.gnu.org/licenses/lgpl.html for license terms.