Revised Cox genetic map, for mouse genome build 39 coordinates.

The original map was with build 37. Markers were shifted so that 0 cM == 0 Mbp. It was later moved to build 38, and at some point we changed it to have 0 cM == 3 Mbp. Shifting to build 39 required dealing with a couple of big inversions at centromeres of chromosome 10 and 14; it seems like the chr 10 one was introduced in build 38 and is now being corrected, while the chr 14 inversion is new.

We used the original Cri-Map software with a few changes to get it to compile; the revised source is on GitHub.

• cox_v3_map.csv - This is the newest Cox genetic map, with build 39 physical positions.

• Data/

  • crimap files used for original Cox map (families split and data cleaned)

• Perl/

  • perl scripts used to prepare and run crimap (using version 2.507 of "CRIMAP Improved")

• R/

  • scripts to merge crimap maps into a CSV file, to reorder the crimap input files, and to combine the genetic and physical maps

• OrigMaps/

  • original (v1 and v2) cox maps

  • combinedmaps_2008-08-06_clean.csv is the original v1 map

  • snpmap_rev_2008-12-10.csv was the v2 map with positions shifted to line up 0 Mbp with 0 cM

  • CoxMaps_rev_build38.csv has build 38 positions added

• Build39/

  • bp coordinates of Cox markers in build 37, 38, and 39

1. Run R/reorder_genfiles.R to create the crimap input files in the build 39 order. Uses Data/final_gen.tgz and creates a set of files in WorkV3/.

   You can similarly run R/subset_genfiles.R. This creates crimap input files in WorkV3b/ that have the subset of markers with build 39 positions, but without reordering the positions.

2. Within the WorkV3/ directory:

   a. Run ../Perl/prepCrimap.pl to run crimap prepare for each of the 20 chromosomes.

   b. Run ../Perl/createCrimapRunFiles.pl. This creates a set of perl scripts plus one bash script, to run crimap for each chromosome (chrompic + sex-averaged and sex-specific maps).

   c. Run runall.sh to run crimap on all chromosomes (simultaneously)

3. Run R/grab_maps.R WorkV3 to grab the estimated map positions and create a combined file map.csv.

4. Copy map.csv to Build39/cox_build39.csv.

5. Run R/combine_maps.R to combine the genetic and physical maps in Build39/ and create the file cox_v3_map.csv.

Licensed under the MIT license. (More information here.)