WHAMM!: Whole-Genome Homozygosity Analysis and Mapping Machina WHAMM...!
Latest WHAMM release is v0.14 (03-Nov-2008)

Whole-Genome Homozygosity Analysis and Mapping Machina

Introduction | Basics | Download | Commands | Usage | Input | Output | Association | Summaries | Permutations | Imputations | FAQ

1. Introduction

2. Basic information

3. Download and general notes

4. Command reference table

5. The Model, Usage, and Pipeline 6. Input Files and Formats 7. Output Files and Formats 8. Association Analysis 9. Data Summaries 10. Permutations 11. Integrated Haplotype Score (iHS) Selection Scan 12. Note on Imputated Data

XX. FAQ & Hints

 

Change Log

This page contains a version/revision history to modifications and additions to WHAMM and to the iHS calculator.

iHS Calculator

v1.0.1 (10-Mar-2011)
  • Modified use of C to C++ libraries for compiling purposes (Thanks to Sébastien Letort for the suggestion)
v1.0 (2009)
  • Initial release.

WHAMM

v0.14a (20-Nov-2008)
  • Bug fixed where R optimization routine was referencing previous program name (hmm_HZmapper.pl not WHAMM.pl).
v0.14 (03-Nov-2008)
  • released v1.0 of iHS Calculator
  • modified WHAMM to perfomr iHS prep and tabulations (--iHS-prep, --iHS-scan, --iHS-subscan, --iHS-std).
  • added a --flip method to construct stand swapped .phased data files and associated .bim files. [not currently implemented with .tped files].
  • added a --chr option for used with --iHS option to calculate scores on specific chromsomes.
v0.13 (10-Oct-2008)
  • updated .R regression machinery to allow bug fixes
  • renamed the machinery "WHAMM" from hmm_HZmapper.pl.
  • modified default file output from "hzmap_out" to "whamm"
v0.12 (23-June-2008)
  • constructed my very first package (.tar.gz)
  • changed directory paths for NSP perl module and .R routines to package path directory.
  • added Cwd.pm module for correct path lookup
  • added some error checking for .R routines before initialization of hmm_HZmapper.pl
  • Fixed static path configuration for hmm_hz_sim_optim_happrobs_v2.R call to a dynamic location
  • Added the genotype/heterozygosity framework. added --gt option, default is to assume phased data model. changed some file preparation steps; notably:
    --phaseloaderfile to --ploaderfile (Assumes .tped file format)
    --hapinfo to --infofile
    --calc-happrobs to --calc-probs
  • Added a speedup/disk space efficiency measure to the regression options --logistic and --linear: only kept samples are output to the transposed .hzdose file fed into R
  • bug fix on get_gtdatafreqs line 2995
v0.11 (20-June-2008)
  • completely revamped the structure of the .R routine to perform regression. Reads in data chunks at a time and performs regression, which can be changed to allow for memory issues if the data set is big (i.e., --make-overlapfile options).
  • modified the .R routine to accept covariates (first order)
  • added --covar option to the mapper, allowing the specification of covariates into the regression
  • changed the functionality of the regression options (--linear and --logistic); now outputs transposed .hzdose files for use with the new .R routine (above)
v0.10 (12-June-2008)
  • added --make-overlapfile option which allows one to essentially merge two data sets with different marker map information
  • fixed an error when no arguments are present on command line (--estimate and $ARGV[0])
v0.09 (04-June-2008)
  • added --linkage option, --dosefile option, changed --regression option to --linear and added a --logistic option.
  • bug corrected on --exttest l option where values != 0.5 weren't obtaining the proper tail angle
  • added .hzlink file format
  • modified hmm_hz_dose_reg.R routine to utilize logistic and linear regression.
  • modified --linear/logistic (formerly --regression) options to process phenotype and keeplists and output processed files sent directly to R (rather than calling R and operating directly on user specified files -- useful for error control)
v0.08 (20-May-2008)
  • Encapsulated existing batch of scripts into a single perl executable, which implements all of the basic features of HZ mapping using phased data.
 

This document last modified Monday, 02-Apr-2012 17:35:45 EDT