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.

Installation and testing

• 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