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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