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Viewing alternate haplotypes with the UCSC Genome Browser

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Published on Dec 9, 2016

This tutorial demonstrates viewing alternate haplotypes with the UCSC Genome Browser. Part 2 of the Multi-Region trilogy. See also https://goo.gl/n8szK2 and https://goo.gl/gQTcyR.

0:17 - Set up the Genome Browser display.
0:34 - View alternate sequences.
1:44 - Fetch sequence of right end of alt.
2:55 - Fetch sequence of left end of alt.
3:18 - Blat the alt ends.
4:37 - Substitute alt ends into chromosome.
6:10 - Track lifted from hg19 lacks hg38 annotations on alt.
6:31 - Remove alt from main chromosome.

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