Simtools

Program to create and process SIM files for the WTSI genotyping pipeline

Executables

simtools
- Create SIM from GTC
- View SIM contents
- Generate input for Illuminus or GenoSNP from SIM
- Compute QC metrics
- Create Illumina Final Call Report (FCR) from GTC
normalize_manifest
- Normalize a .bpm.csv manifest to Illumina TOP strand
sim
- Demonstration program to parse SIM files
g2i
- Older program to convert GTC directly to Illuminus input
- No longer supported
gtc
- Process GTC files for g2i
- No longer supported

Run any executable with --help for more information.

To compile: make all
To run tests: make test. Requires cxxtestgen on the PATH. In the WTSI environment, can use module load cxxtest/$(VERSION).
To install simtools and normalize_manifest: make install PREFIX=$(DESTINATION) will install executables to the bin subdirectory of $DESTINATION.
To install g2i to /software/varinf: make install_g2i

Name		Name	Last commit message	Last commit date
Latest commit History 195 Commits
data		data
json		json
.gitignore		.gitignore
Egt.cpp		Egt.cpp
Egt.h		Egt.h
Fcr.cpp		Fcr.cpp
Fcr.h		Fcr.h
Gtc.cpp		Gtc.cpp
Gtc.h		Gtc.h
Gtc.i		Gtc.i
LICENSE.TXT		LICENSE.TXT
Makefile		Makefile
Manifest.cpp		Manifest.cpp
Manifest.h		Manifest.h
QC.cpp		QC.cpp
QC.h		QC.h
README.md		README.md
Sim.cpp		Sim.cpp
Sim.h		Sim.h
Sim.i		Sim.i
commands.cpp		commands.cpp
commands.h		commands.h
exceptions.h		exceptions.h
g2i.cpp		g2i.cpp
g2v.cpp		g2v.cpp
gtc.cpp		gtc.cpp
gtc_process.cpp		gtc_process.cpp
gtc_process.h		gtc_process.h
gtcdata.json		gtcdata.json
individual.h		individual.h
normalize_manifest.cpp		normalize_manifest.cpp
plink_binary.cpp		plink_binary.cpp
plink_binary.h		plink_binary.h
plink_binary_to_tab.cpp		plink_binary_to_tab.cpp
sim.cpp		sim.cpp
simtools.cpp		simtools.cpp
snp.h		snp.h
tab_to_plink_binary.cpp		tab_to_plink_binary.cpp
test_simtools.h		test_simtools.h
utilities.cpp		utilities.cpp
utilities.h		utilities.h
win2unix.cpp		win2unix.cpp
win2unix.h		win2unix.h