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  • Daniel Lawson
  • Garrett HellenthalDaniel FalushSimon Myers
    • © 2012 Daniel Lawson.
    Website template by Arcsin

    FineSTRUCTURE and ChromoPainter v2 Manual

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

    August 31, 2015

    ∗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 specific parameters
     4.4 Accessing FineSTRUCTURE, ChromoCombine and ChromoPainter directly
     4.5 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 Additional comments