Parameter Name

Parameter Name

Data type

Description

Possible and Default values

leave1mode

Boolean:

In checkit mode, leaves 1 marker at a time and gives the score

NO

dupmode

Boolean

In checkit mode, runs duplicate check on all indivs

NO

fastdup

Boolean

In checkit mode, runs fast duplicate check on all indivs. This parameter is automatically set to YES, in checkit mode

YES

usephyspos

Boolean

Calculates and resets the genetic positions based on physical positions, particularly useful when you don’t have genetic map

NO

dumpgammas

Boolean

Dump gammas for all markers and indivs in binary format (will need another program to print in ASCII format: Alkes)

NO

gammafiles

String

This is the set of files which are created when using dumpgammas

NULL

emiter

Integer

This is the initial EM algorithm to initialize the MCMC

30

alldata

Boolean

Used in simulation mode, make simulated data for all the markers, if NO it keeps the missing data intact

NO

lmmodel

Boolean

Used to run fine-mapping. This assumes ancestry risk is specified by risk model, actually 1D model

NO

lmchrom

Integer

The chromosome on which you run fine-mapping

lmnumx

Integer

Number of points in allele risk mesh

Positive values > 1, default: 30

lmmax

Integer

Max value for the mesh, with number of mesh points being lmnumx

3.0

lmthresh

Double

If fine-mapping log score is below lmthresh, don’t print details of fine-mapping runs

-10.0 (This is to get all the markers)

lmdetails

Boolean

Detailed output

YES

lmlobase

Integer

Physical position low end for fine-mapping

lmhibase

Integer

Physical position high end for fine-mapping

pubxindname

String

Name of a individual for which we want to print some output

pubx

Integer Array

The first component is the internal individual ID for whom you want to output gammas

pubxa

Integer Array

List of individual IDs for which we want to output gamma?

markername

String

This is used to publish the gammas as well as in simulation mode if markersim is not specified

NULL

sim2dvals

Double Array of size 4

Specifies ancestry and allelic risk for fine-mapping simulations

Sim2dvals[0]: Afr freq

Sim2dvals[1]: Caucasian freq

Sim2dvals[2]: λ

Sim2dvals[3] : µ

sim2d_caseonly

Boolean

2D simulation where we only consider the case genotypes?

NO

familynames

Boolean

Used with PED file, if we have unique Indiv Ids set this parameter to NO, else to YES

indivoutname

String

Output file for individual information

snpoutname

String

Output file for marker information

genotypeoutname

String

Output file for genotype data

localoutfilename

String

Output file with all the detailed information for markers

mincasenum

Integer

Removes cases which have below a certain threshold # of genotypes, used in conjunction with the file badpairsname

1

casecontrol

Integer Array

Number of cases and controls, used in simulation mode

hiclip

Double

Allows LOD scores to be upto a maximum of hiclip. Use if scores appear to be saturating

Default: 15.0

loclip

Double

Default: -20.0

packmode

Integer

This packs the genotype data. To be used if one has a memory extensive job

Default: NO