Map making utilities

These utilities consist of awk scripts for creating map files.

mapmarsh.awk	Script to convert a frameworkMap file created by the 'Build your own map' option of the Marshfield Center for Medical Genetics web page (http://www.marshmed.org/genetics/) to a Mega2-format map file. However, note that this will create a map file in Kosambi cM, whereas Mega2 expects a map file in Haldane cM.
mapout.awk	Script to convert from the Mega2-format map file into a format that is easier to edit. This format gives the distances between each pair of adjacent markers, so we will call it the 'intermarker-format'.
kos2hal.awk	Script to convert from an intermarker-format map file in Kosambi cM to a Mega2-format file in Haldane cM.

Example:
Here I illustrate the commands I used to convert some framework map files downloaded from the Marshfield site (which are in Kosambi cM) into Mega2-format map files in Haldane cM.

Comments are in '[  ]' brackets.

NOTES:
1) Make sure you save the files from Marshfield as text-only. The 'mapmarsh.awk' script will not work properly otherwise.
2) You may have to edit the files from Marshfield, as sometime some markers are missing or alternative marker names are used.

 
    watson%	mapmarsh.awk frameworkMap.20 20 > mapk.20
    watson%	mapmarsh.awk frameworkMap.21 21 > mapk.21
    watson%	mapmarsh.awk frameworkMap.22 22 > mapk.22

[So now we have three chromosome specific map files in Kosambi cM. We will place these in one file using the 'cat' command: ]

    watson%	cat mapk.* > map.kos 

[Now we must edit the 'map.kos' file to remove the extra internal title lines.]

    watson%	vi map.kos

[ Convert this file into intermarker-format:]

    watson%	mapout.awk map.kos > mapin.kos

[ Convert the intermarker-format file into a Mega2-format file in Haldane cM: ]

    watson%	kos2hal.awk mapin.kos > map.hal

[ And here it is: ]

    watson%	more map.hal
    Chr      Haldane cM  Name        Haldane  Theta  Kosambi
    20           0.000   D20S103      10.981 0.09859   9.990
    20          10.981   GATA149E11   14.146 0.12321  12.580
    20          25.128   D20S851       8.916 0.08166   8.240
    20          34.043   D20S604       6.707 0.06277   6.310
    20          40.751   D20S470      17.011 0.14419  14.840
    20          57.761   D20S478       8.904 0.08156   8.230
    20          66.666   D20S481      20.622 0.16899  17.590
    20          87.288   D20S480      18.243 0.15285  15.790
    20         105.531   D20S171     
    21           0.000   D21S1432     11.065 0.09926  10.060
    21          11.065   D21S1437     13.032 0.11472  11.680
    21          24.097   D21S1442     13.476 0.11813  12.040
    21          37.573   D21S1440      3.858 0.03713   3.720
    21          41.431   D21S2055     20.208 0.16623  17.280
    21          61.640   D21S1446    
    22           0.000   D22S420      17.553 0.14803  15.260
    22          17.553   D22S1174     10.101 0.09146   9.250
    22          27.654   D22S689       3.966 0.03813   3.820
    22          31.620   D22S685       3.977 0.03823   3.830
    22          35.597   D22S683      10.516 0.09484   9.600
    22          46.113   D22S445     
    watson%	
    script done on Fri Dec 03 16:23:02 1999

Other scripts:

mapin.awk	Script to convert an intermarker-format map file (without the chromosome numbers indicated) into a Mega2-format map file. Handles only files with markers from a single chromosome.
mapin2.awk	Script to convert an intermarker-format map file into a Mega2-format map file. Handles files with markers from multiple chromosomes.
mapmen.awk	Script to convert an intermarker-format map file into a Mendel 4 format map file.
mapsage.awk	Script to convert a Mega2-format map file into a map file in the new SAGE format.
mapsum.awk	Script to rearrange a Mega2-format map file so that the locus name is in the first column.

NOTE:

1. These script were developed quickly for my personal use, and so may not be very robust to unexpected input file formats. Please check the files that are made by these scripts carefully.
2. Under linux, you will need to change the word 'nawk' to the word 'gawk' at the top of each file in order for these scripts to run.
3. The scripts must be executable. Use 'chmod +x script.awk' to make the 'script.awk' file executable.

Creating a Mega2 omit file

The script omit.awk can generate a mega2-format omit file from the error file produced by running Pedcheck. This is strongly recommended in order to identify and remove inconsistent genotypes from the pedigree data.