ARS-UCD1.2 Cow Genome Assembly:
Mapping of all existing variants
Data Repository
Name Size Time Last Modified
UMC_marker_names_180910.zip 215.32 MB2018-09-11 06:37:26
UMC_marker_names_180910.zip.md5 62 B2018-09-11 07:22:04
The NAGRP Data Repository: 2 data files at this location
Data sources/credits:

Data were provided by Robert Schnabel from the University of Missouri:

All of the variants from existing bovine genotyping assays were mapped 
(n%) onto the ARS-UCD1.2 cow genome assembly. All of the data are provided
in the spirit of the Bermuda Principles and Fort Lauderdale Agreement.
https://en.wikipedia.org/wiki/Bermuda_Principles
https://en.wikipedia.org/wiki/Fort_Lauderdale_Agreement

The master file UMC_marker_names_180910.zip can be expanded into 24 each
of the .map, .REF, and .ALLELE files. There is a readme and three files for 
each assay as well as a csv file with all of the raw data and a sql file for 
those who may want to upload the raw data to your favorite RDMS. All of this 
is within a zip file with the date 180910 (YYMMDD). I am providing these 
coordinates to the community to minimize the need for everyone to remap assays 
and hopefully be used as a resource so that everyone can be working off a 
common set of coordinates. I will point out that we intend to perform global 
analyses using these updated coordinates to compare phasing/imputation 
accuracy between the old and new assemblies and ask that everyone respect 
our ability to publish these analyses as part of the manuscript describing 
the new assembly and an accompanying manuscript.

Every attempt was made to ensure that the data are accurate and consistent 
across assays. However, with this volume of data and complexity, there are 
always going to be errors. I would greatly appreciate being notified of any 
errors so that I can verify and correct. If reporting errors/discrepancies, 
please specify the assay, marker_name, and suggested correct coordinates as 
well as the method/evidence supporting the new coordinates. If there are 
enough updates/corrections I will produce an entirely new set of files, with 
a different date.

Contact: Robert Schnabel (schnabelrmissouri.edu)
         University of Missouri
 
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