Structural variation in the IGH region#

Here we visualize PacBio HiFi long-read sequencing data in the immunoglobulin heavy chain (IGH) region, with GENCODE gene annotations. The sequencing data was generated from the HG002 individual from the Genome in a Bottle cohort.

Data sources:

  • PacBio HiFi sequencing: URL

  • Gene annotation: URL

import gzip
import lakeview as lv

CHROMOSOME = "chr14"
VIEW_START = 105679000
VIEW_END = 105776000
START = VIEW_START - int(50e3)
END = VIEW_END + int(50e3)
GENCODE_GFF_PATH = "../../tests/data/gencode.v43.annotation.gff3.gz"
PACBIO_BAM_PATH = "../../tests/data/HG002_IGH_PacBio_CCS.bam"

with gzip.open(GENCODE_GFF_PATH, "rt") as f:
    gencode_painter = lv.GeneAnnotation.from_gencode(
        f, region=(CHROMOSOME, (START, END))
    )
pacbio_painter = lv.SequenceAlignment.from_file(
    PACBIO_BAM_PATH, region=(CHROMOSOME, (START, END))
)
gv = lv.GenomeViewer(3, height_ratios=(1, 8, 2))
pacbio_painter.draw_pileup(
    gv.axes[0],
    show_mismatches=False,
)
pacbio_painter.draw_alignment(
    gv.axes[1],
    show_mismatches=False,
    sort_by="length",
    link_by="name",
    max_rows=50,
)
gencode_painter.draw_transcripts(gv.axes[2], max_rows=5, sort_by="length")

gv.set_xlim((VIEW_START, VIEW_END))
gv.set_xlabel(CHROMOSOME)
gv.set_title("PacBio HiFi long-read sequencing")
../_images/d5e7ccf1529cc57d48647087af621710b7babe70d4382d8983edb6a4b02a3eb0.png 
gv

GenomeViewer(figure=<Figure size 800x800 with 4 Axes>)