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  1. 1. rutgersMap

The rutgersMap database was created from Rutgers Combined Linkage-Phsycal Map1. The current version contains interpolated genetic positions for variants from dbSNP build 134. It is also possible to provide a list of variants with physical positions to the Rutgers Map Interpolator and create your own annotation database using the rutgersMap format with --file option for vtools use command.

Description of the data from Rutgers Computational Genetics Lab:

We have constructed de novo a high-resolution genetic map that includes the largest set of polymorphic markers for which genotype data are publicly available: it combines genotype data from both the CEPH and deCODE pedigrees (for some markers), incorporates SNPs, also incorporates sequence-based positional information. The position of most markers on our map is corroborated by both genomic sequence and recombination-based data. This specific combination of features maximizes marker inclusion, coverage, and resolution, making this map uniquely suited as a comprehensive resource for determining genetic map information (order and distances) for any large set of polymorphic markers.

1.  rutgersMap

% vtools show annotation rutgersMap -v2
Annotation database rutgersMap (version b134)
Description:            Rutgers Combined Linkage-Physical Map
Database type:          position
Reference genome hg19:  chr, position
  position              one-based position in chromosome
  cm_avg                map distance (cM), averaged
  cm_female             map distance (cM), female
  cm_male               map distance (cM), male

1 T. C. Matise, F. Chen, W. Chen, F. M. De La Vega, M. Hansen, C. He, F. C.L. Hyland, G. C. Kennedy, X. Kong, S. S. Murray, J. S. Ziegle, W. C.L. Stewart and S. Buyske (2007). A second-generation combined linkage physical map of the human genome. Genome Research