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human-pangenomics / HPRC_Assembly_Hub

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hg38 tracks on a track hub #5

Open maximilianh opened 1 year ago

maximilianh commented 1 year ago

Hi,

the following things would be good to see on a hg38 track, to give people an idea how HPRC relates to the reference genome. The goal is that a genetics curator can see "does HPRC have anything for me of value in this gene or this exon"

1) Long Variants: long (structural) variants = these are in no database yet. This looks as the most important goal. b) Julian has VCF (?) for this, determine what the format is and load as bigBed, run by Ana Benet Pages and possibly other genetics folks to display in a way optimal for them. c) details page points to HPRC track hub genomes

2) Short Variants: short variants with full phasing using Angie's VCF tree display. These will land in Gnomad but may not yet. a) Julian has VCF for that on hg38 - very easy to load this file

1) genes: not necessary but would be nice = summarize changes that happen to genes a) first find out: is this worth it - how many are affected? b) color genes by whether they change in copy number: no item = no change. Blue = copy increase, red = copy decrease. Details page with links to where they are in HPRC and links to HPRC track hub. c) run by genetics folks like Ana to see if they agree with the display

maximilianh commented 1 year ago

@diekhans

maximilianh commented 1 year ago

@juklucas

diekhans commented 1 year ago

These are tracks for the UCSC hg38 browser @juklucas