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jmonlong / manu-vgsv

https://jmonlong.github.io/manu-vgsv/
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Paragraph: A graph-based structural variant genotyper for short-read sequence data #86

Open jmonlong opened 5 years ago

jmonlong commented 5 years ago

bioRxiv

A quick comparison with our manuscript:

Paragraph Our manuscript
Graph approach Local, extracted reads remapped Whole-genome mapping/calling
Methods benchmarked Delly genotyper, SVtyper, Lumpy, Delly, Manta Delly, SVtyper, BayesTyper, SMRT-SV2
GIAB SV truth set SV called from PacBio GIAB curated SV catalog
SV evaluation SV presence SV presence and genotype
SV evaluation exploration Across size; tandem repeat PR curves; repeats
Delly genotyper benchmark Deletions only Deletions and insertions
SVtyper benchmark SVs > 100bp All SVs
Robust to error in SV bkpt From real data (assuming one is true) Simulation and real data
Read downsampling Depth and read length No
SV catalog (# samples) GIAB (1); ENC002 (1) HGSVC (3); GIAB (3); CHMPD (1); SVPOP (15)
Number of SVs ~17K >60K
Application to a cohort Yes, 100 individuals No
Input SV VCF VCF or genome assemblies

Things I liked and that we should do at some point: evaluation by size (fig2), exploration of breakpoint deviation (fig 3), identification of problematic variants from HWE.