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 [1]
Haploview [12]
WGPermer *[13]

Population stratification

Eigensoft (Eigenstrat, smartPCA) [14]
PLINK [1]
Structure *[15]
Relpair *[16]

Epistasis

PLINK [1]

Imputing

MaCH [24]
IMPUTE [25]

Association analysis of probabilistic genotypes

SNPtest [26]
MaCH2QTL *[24]
ProbABEL *[27]

CNV analysis *

PennCNV [28]
PLINK CNV [1]

Scripting

R scripts [20]
GenABEL *[21]
SAS scripts [22]

Result visualization

Haploview [12]
USCS browser [17]

Mendelian checking of inheritance patterns

PLINK [1]
PEDCHECK [2]
Merlin [3]

Linkage analysis

Merlin [3]
Allegro *[4]
Genehunter [5]
Simwalk2 *[6]
Solar *[7]

TDT analysis

FBAT / PBAT [8,9]
QTDT [10]

Haplotyping

PHASE *[11]
fastPHASE [11]

Pedigree drawing and analysis

Cranefoot [18]
Pelican [19]

Data format conversions

Mega2 *[23]

Data export

ASCII
SPSS
STATA
Excel (SYLK)

For references, please download the list of supported methods.

BC_supported_analysis_programs.pdf (PDF 102 kb)