Genome Browsers
Pennsylvania State University Genome Browser -- Link
Includes
tracks with the variant calls for Venter, Watson, Gates, Church, and the “Irish
Genome” among others.
University of California Santa Cruz Genome Browser
-- Link
Thomas Krahn’s Family Tree DNA Genome Browser -- Link
Especially
useful for mapping SNP names (e.g., M343 or L625) to NCBI36 chrY
positions.
Mapping a single chrY
position between NCBI36 (aka hg18) and GRCh37 (aka hg19)
·
In the “Assembly” input box, select the assembly you
are converting from (NCBI36 or
GRCh37)
·
In the “search term” input box, enter the chrY position you are converting from (e.g., chrY:5419157-5419157)
·
Click the “submit” button
·
On the next screen, click on the “View” pull-down
(right side of the top toolbar)
Note that if the window is too narrow, “View”
will not be visible
·
Select “In Other Genomes (Convert)”
·
In the “New Assembly” input box, select the assembly
you are converting to (NCBI36 or
GRCh37)
·
Click the “submit” button
·
Ensure that “(100.0% of bases, 100.0% of span)” is
present, which indicates there was no problem with the conversion
·
Converted position will be displayed
Mapping multiple chrY positions between NCBI36 (aka
hg18) and GRCh37 (aka hg19)
·
In the “Original Assembly” input box, select the
assembly you are converting from
(NCBI36 or GRCh37)
·
In the “New Assembly” input box, select the assembly
you are converting to (NCBI36 or
GRCh37)
·
Paste the positions to convert into the box labeled
“Paste in data,” then click “Submit”
·
Or select a file containing the positions to convert
using “Upload data from file,” then click “Submit file”
·
In either case, the positions will be listed one per
line in the format chrY:START-END
(e.g., chrY:5419157-5419157)
·
Note that “chrY” must be
specified exactly that way (“ChrY” will fail) and
both START and END positions must be specified
·
Go to the “Results” box, just below where the
positions to convert were entered
·
Ensure there is a “Successfully converted” message
displayed, with no failures indicated
·
Note that the following message is expected and
should be ignored:
Note: "multiple" option is not
supported for position format.
·
Click on “View Conversions” to display the converted
data
International Society of Genetic Genealogy Y-DNA
Haplotree -- Link
Thomas Krahn’s Family Tree DNA Draft Y-DNA Haplotree -- Link
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owners.
Copyright © 2011-2012 David F Reynolds
Licensed under a Creative
Commons Attribution-ShareAlike 3.0 License.
Last Modification: 24 Aug 2012