kbroman / CoxMapV3

Revised Cox et al. mouse genetic map, for build 39 of the mouse genome

Cox genetic map V3

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

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Outline of analysis

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.

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License

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