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  • Daniel Lawson
  • Garrett HellenthalDaniel FalushSimon Myers
    • © 2012 Daniel Lawson.
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    FineSTRUCTURE and ChromoPainter v2 Manual

    Daniel John Lawson*
    dan.lawson@bristol.ac.uk

    May 21, 2018

    *Integrative Epidemiology Unit, School of Social and Community Medicine, and Department of Statistics, University of Bristol, UK
    About
    Contents
    1 Changes from Version 0
    2 How to use this software
    3 Overview of FineSTRUCTURE and the help system
     3.1 Information about the processing pipeline
     3.2 Basic Help for ‘automatic mode’
    4 Detailed help
     4.1 Information on Input formats
     4.2 Help on how the computation is performed
     4.3 Help on the output files created
     4.4 Help on specific parameters
     4.5 Accessing FineSTRUCTURE, ChromoCombine and ChromoPainter directly
     4.6 List of all parameters
    5 ChromoPainter
    6 ChromoCombine
    7 FineSTRUCTURE
    8 Computational considerations
    9 Greedy finestructure
    10 Job submission in qsub and related environments
    11 Provided scripts
     11.1 makeuniformrecfile.pl
     11.2 convertrecfile.pl
     11.3 chromopainter2chromopainterv2.pl
     11.4 phasescreen.pl
     11.5 phasesubsample.pl
     11.6 plink2chromopainter.pl (PLINK)
     11.7 impute2chromopainter.pl (SHAPEIT format)
     11.8 beagle2chromopainter.pl (BEAGLE format)
     11.9 msms2cp.pl (MSMS and MS output format)
    12 Potential pitfalls
    13 Examples
     13.1 Simple and quick example
     13.2 Involved example with few SNPs and individuals
     13.3 HGDP example, including downloading and processing.
    14 Additional comments