Hightlight variants in PAR regions

Clinical-Genomics-Lund / gens

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Hightlight variants in PAR regions #142

Open mhkc opened 11 months ago

mhkc commented 11 months ago

Highlight variants that are int PAR regions in Gens.

PAR_COORDINATES = {
    "37": {
        "X": IntervalTree(
            [Interval(60001, 2699521, "par1"), Interval(154931044, 155260561, "par2")]
        ),
        "Y": IntervalTree([Interval(10001, 2649521, "par1"), Interval(59034050, 59363567, "par2")]),
    },
    "38": {
        "X": IntervalTree(
            [Interval(10001, 2781480, "par1"), Interval(155701383, 156030896, "par2")]
        ),
        "Y": IntervalTree([Interval(10001, 2781480, "par1"), Interval(56887903, 57217416, "par2")]),
    },
}

TJO-Lund commented 11 months ago

Korrekta PAR positioner på X resp. Y (vad jag kan bedöma och stämmer med pos. i ChAS) är: https://www.ensembl.org/info/genome/genebuild/human_PARS.html

chromosome:GRCh38:Y:10001 - 2781479 is shared with X: 10001 - 2781479 (PAR1)
chromosome:GRCh38:Y:56887903 - 57217415 is shared with X: 155701383 - 156030895 (PAR2)

Förslagsvis med ljusröd transparent skuggning i kromosomvy i Gens, så att bef. bandning syns igenom (jmf med ChAS)