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)

·        Go to the Brower Entry page

·        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)

·        Go to the Batch Coordinate Conversion (liftOver) page

·        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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Last Modification: 24 Aug 2012