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Validations
Darren J. Lin edited this page Mar 3, 2021
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In this study, we have done intensive experimental and computational validations as well as manual inspections of Mako CSVs from HG00733 (609 events). The experimental validation was done through PCR and Sanger sequencing. The computational validation contained ONT reads based VaPoR (https://github.com/mills-lab/vapor) validation and HiFi contigs based K-mer validation. The ONT reads and the latest HiFi contigs were obtained from Human Genome Structural Variant Consortium (HGSVC).
HG00733 haploid HiFi assembly
HG00733 Oxford Nanopore sequencing
Please refer to the VaPoR (https://github.com/mills-lab/vapor) GitHub repo.
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Chrom | Start | End | PacBio Type |
---|---|---|---|
chr1 | 81,194,398 | 81,195,874 | invDup |
chr2 | 119,659,504 | 119,661,322 | insDup |
chr3 | 146,667,093 | 146,677,284 | delDisDup |
chr5 | 141,480,327 | 141,483,116 | disDup |
chr7 | 1,940,931 | 1,941,009 | insDup |
chr9 | 29,591,409 | 29,593,057 | delINV |
chr10 | 14,568,488 | 14,568,677 | insDup |
chr12 | 71,315,482 | 71,316,928 | invDup |
chr12 | 77,989,900 | 77,994,324 | invDup |
chr13 | 74,340,759 | 74,342,810 | disDup |
chr16 | 78,004,459 | 78,007,456 | disDup |
chr17 | 34,854,438 | 34,855,851 | invDup |
chr17 | 48,538,270 | 48,540,171 | disDup |
chr18 | 72,044,575 | 72,045,937 | disDup |
chr21 | 26,001,844 | 26,002,990 | delINV |
Strategy | Valid |
---|---|
PCR and Sanger sequencing | 68% |
ONT reads | 42% |
HiFi contig | 68% |
ONT reads or HiFi contig | 87% |