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

 

Options

Basic input/output
Option Parameter/default Required Input Description
--samplefile {whamm.sinfo} Specify sample information file
--segfile {whamm.smap} Specify a segment map file [.smap]
--ploaderfile {whamm.pload} Specify a phased haplotype loader file [.pload]
--pheno {phenofile} Specify a phenotype file
--out {whamm} Specify output root filename
--infofile {whamm.hinfo or whamm.ginfo} Specify the frequency information file, either haplotype [.hinfo] or genotype [.ginfo]
--paintfile {whamm.fbpath} Specify the forward/backward path file [.fbpath]
--keep {keeplistfile} Specify a list of samples to include
--paramsfile {paramsfile.params} Specify a list of estimated parameters (f,a)
--covar {covariatefile.txt} Specify a list covariates (used in --logistic or --linear options)
--dosefile {whamm.hzdose} Specify the HZ dosage file[.hzdose]
     
Analysis Preparation procedures
Option Parameter/default Required Input Description
--make-infofiles {hotspot.list} {cMmapfile.map/.bim} {.sinfo} {.pload}Calculates segment map and haplotype frequencies [.smap and .hinfo]
--calc-probs {.smap} {.hinfo or .ginfo} {.sinfo} {.pload}Calculates Haplotype Probabilities [.hzprobs]
--paint {probs.hzprobs} {.smap}Calculates (f,a) parameters from the model [.params], and ouputs forward/backward path [.fbpath] (R Routine Call)
--fbprobs Reports forward/backward probabilities [.hzdose]
--make-overlapfiles {set2.sinfo} {set2.smap} {set2.hzdose} {set2.fbpath} {.sinfo} {.smap} {.hzdose} {.fbpath}Outputs a joint .hzdose, .fbpath. and .smap file from two data sets with different segment maps
     
Association Analysis procedures
Option Parameter/default Required Input Description
--exttest{dir: [l|h]} {tailval: [0-1]} {restval: [0-1]}{.sinfo} {.smap} {.fbpath} {phenofile}Perform Fisher's Exact Test of Homozygosity in QTL Extremes vs. Opposite Tail [.hzassoc]
--fisher{.sinfo} {.smap} {.fbpath} {phenofile}Perform Fisher's Exact Test of Homozygosity in Cases vs. Controls [.hzassoc]
--linear {.sinfo} {.smap} {.hzdose} {phenofile}Perform linear regression using HZ dose information [.hzdassoc] (R routine call)
--logistic{dir: [l|h]} {tailval: [0-1]} {restval: [0-1]} or {dir: b}{.sinfo} {.smap} {.hzdose} {phenofile}Perform logistic regression in QTL Extremes vs. Opposite tail [(l)ow and (h)igh options] or on (b)oolean phenotype using HZ dose information [.hzdassoc] (R routine call)
     
iHS Statistics options
Option Parameter/default Required Input Description
--iHS-prep {ancstates.txt rhomap.gmap} {.sinfo} {.pload}Construct .data and .info files for iHS scan
--iHS-scan {ihsfile.info ihsfile.data} {ihs.info} {ihs.data}Calculate unstandardized iHS score for all markers in .info file [.ihs]
--iHS-subscan {ihsfile.info ihsfile.data start end} {ihs.info} {ihs.data}Calculate unstandardized iHS score for markers start to end inclusive in .info file [.ihs]
--iHS-std {ihsstdfile.txt ihsresfile.ihs} Calculate standardized iHS from unstandardized iHS results file [*_std.ihs]
     
Summary Statistics options
Option Parameter/default Required Input Description
     
Miscellaneous Helper options
Option Parameter/default Required Input Description
--missing-phenotype {missval} Specify a missing phenotype value
--flip {fliplist mapfile.bim} {.pload}Strand flips phased data and .bim map file
     
 

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