NanoCaller for accurate detection of SNPs and indels in difficult-to-map regions from long-read sequencing by haplotype-aware deep neural networks

Ahsan, Mian Umair; Liu, Qian; Fang, Li; Wang, Kai

doi:10.1186/s13059-021-02472-2

Table 1 Performances (F1 scores in %) of SNP and indel predictions by NanoCaller, Medaka, Clair, Longshot, and DeepVariants on ONT and PacBio (CCS and CLR) datasets. This evaluation is based on v3.3.2 benchmark variants for HG001 and HG005-7, and v4.2.1 benchmark variants for the Ashkenazim trio (HG002, HG003, and HG004). Bonito and R10.3 refer to different versions of the HG002 ONT datasets

From: NanoCaller for accurate detection of SNPs and indels in difficult-to-map regions from long-read sequencing by haplotype-aware deep neural networks

Prediction	Variant caller	HG001	HG002	HG003	HG004	HG005	HG006	HG007	HX1	Bonito	R10.3
SNPs on ONT data in high-confidence intervals	NanoCaller ONT-HG001	98.58	98.35	98.99	98.97	98.10	98.23	97.81	98.45	99.33	98.28
	NanoCaller ONT-HG002	98.63	98.66	99.09	99.11	98.38	98.43	98.06	98.60	99.34	98.44
	Medaka	99.03	98.59	99.02	99.04	98.17	98.50	98.24	98.94	99.24	96.94
	Clair	98.79	97.77	98.60	98.58	97.73	97.90	97.50	98.53	98.75	90.44
	Longshot	98.78	98.03	97.88	97.90	98.34	98.53	98.51	98.59	98.59	98.18
Indels on ONT data in high-confidence intervals	NanoCaller ONT-HG001	57.33	53.94	58.52	57.71	56.31	56.14	53.78	73.67	62.07	61.59
	NanoCaller ONT-HG002	56.69	54.37	58.47	57.69	56.93	56.56	54.44	73.90	61.17	60.56
	Medaka	48.67	48.10	53.59	50.19	55.89	52.49	51.83	81.13	51.03	53.09
	Clair	49.72	47.64	52.06	51.20	52.58	51.90	50.63	80.59	50.11	44.80
Indels on ONT data in non-homopolymer regions	NanoCaller ONT-HG001	87.65	82.28	87.93	87.93	81.92	85.70	83.41	59.47	86.12	84.43
	NanoCaller ONT-HG002	87.19	82.80	87.93	88.04	82.60	86.10	83.92	59.17	85.76	83.51
	Medaka	82.07	78.70	85.74	84.23	80.97	84.41	82.91	55.17	78.24	78.75
	Clair	75.25	70.06	75.55	74.85	72.60	75.92	75.04	58.43	70.99	62.93
SNPs on PacBio CCS data in high-confidence intervals	NanoCaller CCS-HG001	99.25	99.80	99.79	99.71
	NanoCaller CCS-HG002	99.17	99.80	99.79	99.75
	Clair	99.66	99.84	99.72	99.79
	Longshot	99.37	99.03	99.05	99.05
	DeepVariant	99.82	99.93	99.91	99.84
Indels on PacBio CCS data in high-confidence intervals	NanoCaller CCS-HG001	92.67	93.30	93.42	93.10
	NanoCaller CCS-HG002	93.13	94.10	94.34	93.97
	Clair	94.87	96.71	97.51	95.57
	DeepVariant	98.21	99.28	99.48	98.42
SNPs on PacBio CLR data in high-confidence intervals	NanoCaller CLR-HG002	94.42	98.75	94.41	93.41
	Clair	95.83	98.38	94.89	94.15
	Longshot	96.81	98.41	94.35	93.27

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