Supported Analysis Methods

For the following methods BC Platforms offers graphical web browser user interfaces, analysis job segmentation tools, automated workflow for running the analysis on a calculation cluster, or alternatively exporting of data as analysis program input files. The programs marked with an asterisk (*) are available upon request.

Case-control analysis

PLINK
Haploview
WGPermer *

Population stratification

Eigensoft (Eigenstrat, smartPCA)
PLINK
Structure *
Relpair *

Epistasis

PLINK

Imputing

MaCH
IMPUTE
BEAGLE *
Minimac *

Association analysis of probabilistic genotypes

SNPtest
MaCH2QTL *
ProbABEL *

CNV analysis *

PennCNV
PLINK CNV

Scripting

R scripts
GenABEL *
SAS scripts

Result visualization

Haploview
USCS browser
GWAScentral

Mendelian checking of inheritance patterns

PLINK
PEDCHECK
Merlin

Linkage analysis

Merlin
Allegro *
Genehunter
Simwalk2 *
Solar *

TDT analysis

FBAT / PBAT
QTDT

Haplotyping

PHASE *
fastPHASE

Pedigree drawing and analysis

Cranefoot
Pelican

Data format conversions

Mega2 *

Data export

ASCII
SPSS
STATA
Excel (SYLK)


The complete list with references can be also viewed and downloaded here (PDF 91 kb) .