1BP_COMPOSITE_LD(1)    User Contributed Perl Documentation   BP_COMPOSITE_LD(1)
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NAME

6       composite_LD -i filename.prettybase.txt --sortbyld > outfile
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SYNOPSIS

9         composite_LD -i filename.prettybase [-o out.LD] [-f prettybase/csv] [--sortbyld] [--noconvertindels]
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11       DESCRIPTION
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13       This a script which allows an easy way to calculate composite LD.
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15       OPTIONS
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17       -i or --in     filename
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19       -f or --format genotype format (prettybase or CSV)
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21       --sortbyld     To see data sorted by LD instead of just all the
22                      site1/site2 pair LD values.
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24       -o or --out    output filename, otherwise will print to STDOUT
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26       --noconvert    (applicable for prettybase format file only)
27                      if specified will NOT attempt to convert indel
28                      states to 'I' and delete states ('-') to 'D'.
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30       -h or --help   see this documentation
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32       AUTHOR Jason Stajich, Matthew Hahn
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34       For more information contact:
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36       Matthew Hahn, <matthew.hahn-at-duke.edu> Jason Stajich <jason-at-biop‐
37       erl-dot-org>
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41perl v5.8.8                       2007-05-07                BP_COMPOSITE_LD(1)
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