ALOHOMORA Copyright (c) 2003-2009 Franz Rüschendorf UPGRADES ------------------------------------------------------------------------------- ALOHOMORA_M v0.33 21-Oct-2009 Fixed bug: Chip type selection "GW6". Map file was not loaded. Function "Utilities -> Calling rate" (by sample) revised -------------------------------------------------------------------------------- ALOHOMORA v0.32 11-Aug-2009 ALOHOMORA_M v0.32 11-Aug-2009 Filter functions revised Function "Calculate Allele frequencies,Callrate,HWE" revised (output format) Implemented: Chip selection "GW6" and "Illumina300" (only in Alohomora_M) -------------------------------------------------------------------------------- ALOHOMORA_M v0.31 27-Jul-2009 Implemented: Menubar-> Options -> Alias names Fixed bug: in option "Select markers for Linkage analysis" and skiplist together ALOHOMORA v0.31 27-Jul-2009 Fixed bug: create folder without w/r/x permissions in Linux, Solaris version -------------------------------------------------------------------------------- ALOHOMORA_M v 0.30_R3 02-Apr-2007 Implemented: Menubar-> Options -> Select markers for linkage analysis -------------------------------------------------------------------------------- ALOHOMORA_M v 0.30_R2 21-Mar-2007 Fixed bug: In some cases the data conversion into linkage format files does not include all markers from the X-chromosome -------------------------------------------------------------------------------- ALOHOMORA_M v 0.30 02-Mar-2007 For Mega-Chips ALOHOMORA_M is a slow version of ALOHOMORA which reads genotype data step by step in the way of a moving window from many files. This makes ALOHOMORA_M nearly unlimited to the number of markers. The amount of markers loaded simultaneously is user-specified by the variable LOAD_SIZE in alohomora.ini and depends on the number of samples in the project and the computers RAM. The format of the genotype data file has changed in ALOHOMORA_M (not in ALOHOMORA)! Now original GTYPE or GDAS output files will be loaded. The column containing the marker name is identified by the column header "SNP ID" and all columns containing genotypes must have an ending "_Call" in their header. There may be additional columns, not being the marker name or genotypes, in this file. The number of genotype data files is not restricted. Two or more genotype data files are specified with a wild-card (e.g. TableData_*.txt). Implemented: Menubar-> DataConversion-> PLINK Menubar-> Help -> Show Help BATCH-modus Not yet implemented: Menubar-> Options -> Alias names Menubar-> Options -> Select markers for linkage analysis -------------------------------------------------------------------------------- ALOHOMORA v 0.30 02-Mar-2007 New features: Menubar-> DataConversion-> PLINK Data conversion to the PLINK program, the "Whole genome association analysis toolset" (http://pngu.mgh.harvard.edu/~purcell/plink/) Menubar-> Options -> Alias names Use the rs-number instead of the Affymetrix SNP ID for Linkage format data output. Menubar-> Options -> Select markers for linkage analysis The markers for a linkage analysis can be selected by two ways: 1. a) minimal distance between markers and b) minimal minor allele frequency. 2. By chromosome, first and last position (in bases) A combination of way 1 and 2 is possible. ALOHOMORA can be started optionally in BATCH-modus with the argument --nogui usage: alohomora [] Options: --nogui batch modus --help|-?|-h this help\n"; -p file containing the pedigree structure and affection status -g file containing the genotype calls -b alohomora batch file When started ALOHOMORA reads at first variables from alohomora.ini (if available), commmand line vaiables overwrite alohomora.ini variables, then, if --nogui is specified ALOHOMORA tries to read commands from alohomora.bch. Menubar-> Help -> Show Help A short description of the ALOHOMORA input file format. -------------------------------------------------------------------------------- ALOHOMORA v 0.29_R2 22-Feb-2006 New features: Alohomora creates now Merlin format map files for sets of markers merlin_map_. The script "merlin_scan_start.pl" starts Merlin with a moving window. -------------------------------------------------------------------------------- ALOHOMORA v 0.29 12-Jan-2006 New features: Menubar-> Options-> Phenotype selection Alohomora handles quantitative trait values (QTL) for Linkage Analysis with Genehunter or Merlin. Menubar-> Options-> GRR marker selection When using the 50/100K or 250/500K chip the amount of markers is too much for the program Graphical Relationship Representation (GRR). May be 3000 markers are enough. The user limits the amount of markers by the options: 1. minimal distance between markers and 2. minimal minor allele frequency. Menubar-> DataConversion-> FBAT Data conversion to the Family Based Association Test (FBAT) format Genetic maps and allele frequency files are provided for the Affymetrix chips 10K (Xba131), 10Kv2 (Xba142), 50K (Xba240 and Hind240) and 250K (Nsp and Sty), as well as for the Illumina LinkageIV panel. The genetic maps for the Affymetrix SNP panels were extracted from the SNP annotation CSV-files (e.g. http://www.affymetrix.com/support/technical/byproduct.affx?product=100k), where SNP integration into genetic maps were based on NCBI build35. The annotation files for the Illumina Linkage IV panel and the Perl-script "illumina2affy.pl" were provided by Tim Strom (GSF, Neuherberg, email: TimStrom@gsf.de). The genetic map file "LinkageIV_map_decode_2005-02-21.txt" is based on NCBI build34. The script "illumina2affy.pl" converts the Illumina genotype output file into a format for ALOHOMORA. -------------------------------------------------------------------------------- ALOHOMORA v 0.28 10-Mar-2005 New features: Menubar-> Check-> Compare sampleIDs Shows doubled sampleIDs in pedfile.pro or genotype file. Shows sampleIDs in pedfile.pro, but not in genotype file Shows sampleIDs in genotype file, but not in pedfile.pro Menubar-> Utilities-> PedStat Pedfile summary statistic -------------------------------------------------------------------------------- ALOHOMORA v 0.27 18-Jan-2005 A TSC-number of "TSC1234" will be converted to "tsc0001234". The GDAS genoptype export file may have different formats of the TSC-number. There are GDAS versions (or SNPannotation libraries) writing the TSC-number in uppercase or lowercase letters and with or w/o leading zeros. The format in the genetic maps is lowercase "tsc" and 7 digits with leading zeros. -------------------------------------------------------------------------------- ALOHOMORA v0.26 first release