Generic solutions for specific problems
Johannes Köster
Harpoon 2022
Variant calling
Varlociraptor
species:
heterozygosity: 0.001
ploidy:
male:
all: 2
X: 1
Y: 1
female:
all: 2
X: 2
Y: 0
samples:
normal:
sex: female
somatic-effective-mutation-rate: 1e-10
tumor:
inheritance:
clonal:
from: jane
contamination:
by: jane
fraction: 0.1
somatic-effective-mutation-rate: 1e-6
events:
germline: "normal:0.5 | normal:1.0"
somatic_normal: "normal:]0.0,0.5["
somatic_tumor_low: "normal:0.0 & tumor:]0.0,0.1["
somatic_tumor_high: "normal:0.0 & tumor:[0.1,1.0]"
- technology-agnostic (short, long, dna, rna)
- small and structural variants
- fully uncertainty aware
- integrated bias estimation
- no technical parameters
Input:
- aligned reads
- candidate variants
- scenario
Output:
- variant calls
- evidence details
- posterior probability of events
- FDR control instead of tuning score thresholds
Genomic variant presentation
Datavzrd
views:
coding-variants:
dataset: coding-variants
render-table:
columns:
symbol:
link-to-url: https://www.ensembl.org/Homo_sapiens/Transcript/Summary?t={feature}
hgvsp:
custom-path: resources/varsome-link.js
vartype:
display-mode: hidden
consequence:
plot:
heatmap:
color-scheme: category20
scale: ordinal
read-depth:
plot:
ticks:
scale: linear
Input:
- set of tables
- config with
- relations
- column rendering specs
- custom plot specs
Output:
- interactive, self-contained HTML
- search & filter
- export to PDF and Excel
johannes.koester@uni-due.de
Generic solutions for specific problems
By Johannes Köster
Generic solutions for specific problems
Talk at ETIM 2022
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