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
PLINK multivariate *
Haploview
WG-Permer *
METAL *
HAPPY *
QCtool *

Population stratification

Eigensoft (Eigenstrat, smartPCA)
PLINK
Structure *
Relpair *

Epistasis

PLINK
BEAM *

Imputing

MaCH
IMPUTE *
BEAGLE *
Minimac *

Association analysis of probabilistic genotypes

SNPtest
MaCH2QTL *
ProbABEL *

Next Generation Sequencing (NGS)*

PLINK/SEQ
ANNOVAR
Granvil
PolyPhen2
SIFT *
SAMtools
Data export/import in the Variant Call Format (VCF)

CNV analysis *

PennCNV
PLINK CNV
QuantiSNP *

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 171 kb) .