Map file

Description

Map file contains information about markers: chromosome, location, order and name of the marker. File format described here is used by Mega2 converter program, since mega2 used often to make SimWalk2 input files. Many in-house program uses this format as well.

Format

Map file is general ASCII-text file (created with notepad or some other text editor) and it contains header line and three columns.

Header line

    Chromosome   Haldane   Name

Second column in header line specifies map function (haldane or kosambi) used in conversion from cM to recombination fraction (needed for some programs). Columns after header line:

    Column 1: Chromosome number         
    Column 2: Location              (continuous cM-map)
    Column 3: Name of the marker

Example of chromosome 7 with 6 markers:

    Chromosome   Haldane    Name
    7            0          D7S2233
    7            2          ATA100
    7            6          D7S9339
    7            11         WATR567
    7            11.9       D7S1122
    7            15         D7S5566

Markers distances are in cM (centi-morgans) and map is continuous. Map does not have to start from 0 cM. Markers have to be in same order in pedigree file.

Last line of the file must be empty line!

Naming of the files

It's recommended to have each chromosome in separate file and name files according to chromosme as map1.dat, map2.dat, ..., map22.dat

More info

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