Description

CRI-MAP is designed to allow rapid, largely automated construction of multilocus linkage maps (and facilitate the attendant tasks of assessing support relative to alternative locus orders, generating LOD tables, and detecting data errors). It was developed by Phil Green at the University of Washington.

CRIP-MAP is intended to be used interactively on Helix. To run a CRI-MAP job, log on to helix.nih.gov using ssh, and type crimap

Sample session

Sample file chr7a.gen can be copied from /usr/local/src/crimap

% crimap 7a prepare

chromosome 7a

50400 bytes allocated in orders_morecore

No .dat file named chr7a.dat

504000 bytes allocated in morecore

Creating .dat file chr7a.dat from .gen file chr7a.gen

504000 bytes allocated in morecore

family id 12
family id 66
family id 102
family id 104
family id 884
family id 13291
family id 13292
family id 13293
family id 13294
family id 1331
family id 1332
family id 1333
family id 1334
family id 1340
family id 1341
family id 1344
family id 1345
family id 1346
family id 1349
family id 1350
family id 1362
family id 1375
family id 1377
family id 1408
family id 1413
family id 1416
family id 1418
family id 1420
family id 1421
family id 1423
family id 1424

Writing file chr7a.dat


Finished writing chr7a.dat

Writing locus names to chr7a.loc

Current values for parameters:

par_file = chr7a.par
dat_file = chr7a.dat
gen_file = chr7a.gen
ord_file = chr7a.ord
nb_our_alloc = 3000000    [# bytes reserved for our_alloc]
SEX_EQ = 1   [0 = sex specific analysis, 1 = sex equal]
TOL = 0.010000
PUK_NUM_ORDERS_TOL = 6
PK_NUM_ORDERS_TOL = 8
PUK_LIKE_TOL = 3.000
PK_LIKE_TOL = 3.000
use_ord_file = 0
write_ord_file = 1
use_haps = 1

Do you wish to change any of these values? (y/n) n

The loci and their indices are:

  0   'LOCX                 1   'D7COL-HAP-A          2   'D7MET-HAP-A

  3   'D7S8-M-A             4   'D7TCRB-BG-A          5   'L281-HAP-A

  6   'L0281-T-A            7   'L0544-M-A            8   'L0751-M-A

  9   'L0887-M-A           10   'L0917-HAP-A         11   'L0966-R-A

 12   'L1020-T-A           13   'L1020-HAP-A         14   'L1033-M-A

 15   'R0012-M-A           16   'R0040-M2-A

Do you wish to enter any new haplotyped systems? (y/n) n

Do you wish to hold any additional recombination fractions fixed (NB
these will
only be used with the options FIXED and CHROMPIC, and only when the
loci in question
 are adjacent)? (y/n) y

For each new fixed rec. frac. which you wish to enter, type
fixed_dist, followed
by the recombination fraction, followed by the indices of the loci
followed by the sex (0 for females, 1 for males) if the forced
distance is to apply to one
sex only, followed by * and a carriage return.  Example:

fixed_dist 0.5 0 5 * [Return]

When you are done, type

done [Return]

To modify or delete a previously
entered system, you will need to edit the .par file later with a text
editor.
Ready:
done

The crimap options are:

[1] build  [2] instant  [3] quick  [4] fixed

[5] flips  [6] all  [7] twopoint  [8] chrompic

Enter the number of the option you will be running next: 1

Do you wish to build the map incorporating ALL loci in decreasing
order of
their informativeness (the usual procedure)? (y/n) y

The loci and their indices are:

 13   'L1020-HAP-A         11   'L0966-R-A           12   'L1020-T-A

 10   'L0917-HAP-A          5   'L281-HAP-A           8   'L0751-M-A

  2   'D7MET-HAP-A          9   'L0887-M-A            0   'LOCX

  7   'L0544-M-A           16   'R0040-M2-A           1   'D7COL-HAP-A

 14   'L1033-M-A           15   'R0012-M-A            3   'D7S8-M-A

  4   'D7TCRB-BG-A          6   'L0281-T-A

Creating orders file chr7a.ord

Done.

OK to set up new parameter file? (y/n) y

chr7a.par has been created; use text editor for further modifications,
if needed

% ls -l
-rw-r--r--   1 user user  36867 Aug 25 16:17 chr7a.gen
-rw-r--r--   1 user user  31586 Aug 25 16:18 chr7a.dat
-rw-r--r--   1 user user    872 Aug 25 16:18 chr7a.loc
-rw-r--r--   1 user user     18 Aug 25 16:18 chr7a.ord
-rw-r--r--   1 user user    338 Aug 25 16:20 chr7a.par

%crimap 7a twopoint
chromosome 7a
50400 bytes allocated in orders_morecore
3024000 bytes allocated in morecore
Option chosen: twopoint

Current values for parameters:

par_file = chr7a.par
dat_file = chr7a.dat
gen_file = chr7a.gen
ord_file = chr7a.ord
nb_our_alloc = 3000000    [# bytes reserved for our_alloc]
SEX_EQ = 1   [0 = sex specific analysis, 1 = sex equal]
TOL = 0.010000
PUK_NUM_ORDERS_TOL = 6
PK_NUM_ORDERS_TOL = 8
PUK_LIKE_TOL = 3.000
PK_LIKE_TOL = 3.000
use_ord_file = 0
write_ord_file = 0
use_haps = 1

'L1020-HAP-A        'L0966-R-A

AGAINST:

'L1020-T-A          'L0917-HAP-A        'L281-HAP-A         'L0751-M-A
         'D7MET-HAP-A
'L0887-M-A          'LOCX               'L0544-M-A
'R0040-M2-A         'D7COL-HAP-A
'L1033-M-A          'R0012-M-A          'D7S8-M-A
'D7TCRB-BG-A        'L0281-T-A

'L1020-HAP-A   'L1020-T-A  rec. fracs.=    0.00,   lods =   58.05
  57.72  57.90  54.85  50.26  45.26  39.91  34.19  28.07  21.52  14.54
    7.25   0.00

'L1020-HAP-A   'L0751-M-A  rec. fracs.=    0.26,   lods =    5.86
 -77.50 -36.99 -10.54  -1.07   3.15   5.14   5.83   5.66   4.85   3.56
   1.90   0.00

'L1020-HAP-A   'L0887-M-A  rec. fracs.=    0.27,   lods =    4.39
 -67.42 -32.81 -10.15  -1.95   1.77   3.59   4.32   4.31   3.75   2.75
   1.45   0.00

'L1020-HAP-A   'R0012-M-A  rec. fracs.=    0.13,   lods =    9.34
 -11.35   0.34   7.32   9.10   9.30   8.80   7.87   6.63   5.15   3.48
   1.72   0.00

'L0966-R-A   'L281-HAP-A  rec. fracs.=    0.05,   lods =   34.95
  22.00  31.27  34.94  33.66  30.94  27.53  23.65  19.40  14.81   9.92
    4.87   0.00

'L0966-R-A   'L0281-T-A  rec. fracs.=    0.00,   lods =    3.31
   3.31   3.25   3.00   2.69   2.36   2.03   1.70   1.36   1.02   0.68
     0.34   0.00

Documentation

CRI-MAP Documentation at the Rockefeller Linkage site.