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Fig. 1 | Genome Medicine

Fig. 1

From: Whole-genome sequencing with long reads reveals complex structure and origin of structural variation in human genetic variations and somatic mutations in cancer

Fig. 1

Result of benchmarking using NA19240. Indels (≥ 100 bp) were identified with several software from the fastq file of NA19240 and compared with a gold standard SV callset as performed previously [13]. We classified SVs as common; detected in gold standard SV calls and each caller, gold standard SV call only; detected only in gold standard SV calls and caller only; detected only in each caller. SVs in “gold standard SV call only” were considered false negatives and “caller only” false positives, and F-measures were calculated with sensitivity and specificity. SVs were classified based on repeat information of regions. SVs in tandem repeat regions, self-chain regions, regions in both repeats, and non-repeat regions were evaluated separately. “CAMPHOR” was a result of parameter setting in this study, and “CAMPHOR (appropriate parameter set for 20× data)” was a result of the released version

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Genome Medicine

ISSN: 1756-994X

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