ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly

Table 1 Indel detection (bp) by diffferent methods with 2 × 300-bp amplicon sequencing reads

Data set 1	Gene	Mutation	Tissue	Mean coverage	PCR/CE	ScanIndel	GATK	Pindel	Scalpel	Platypus	FermiKit	Delly
1-1	CALR	DEL	BM	46,913	52	52	52	NC	NC	NC	NC	NC
1-2	EGFR	DEL	FFPE	25,821	18	18	18	NC	NC	18	NC	NC
1-3	KIT	DEL	FFPE	12,990	6	6	6	NC	NC	6	NC	NC
1-4	NPM1	INS	BM	21,387	4	4	4	4	NC	NC	NC	NC
1-5	FLT3	INS	BM	4768	21	21	21	21	NC	NC	NC	NC
1-6	FLT3	INS	BM	11,510	26	27	NC	27	NC	NC	NC	NC
1-7	FLT3	INS	BM	26,747	49	51	NC	51	NC	NC	NC	NC
1-8	FLT3	INS	BM	28,991	38	39	NC	39	NC	NC	NC	NC
1-9	FLT3	INS	BM	26,734	90	93	NC	93	NC	NC	93	NC
1-10	FLT3	INS	BM	16,152	75	78	NC	78	NC	NC	NC	NC
1-11	FLT3	INS	BM	3528	32	33	33	33	NC	NC	NC	NC
1-12	FLT3	INS	BM	3851	51	54	54	54	NC	NC	NC	NC
1-13	FLT3	INS	BM	21,403	23	24	24	24	NC	NC	NC	NC
1-14	FLT3	INS	BM	3070	45	48	48	48	NC	NC	NC	NC
1-15	FLT3	INS	BM	4506	33	36	36	36	NC	NC	NC	NC
1-16	FLT3	NEG	BM	4471	NC	NC	NC	NC	NC	NC	NC	NC
1-17	FLT3	NEG	BM	4321	NC	NC	NC	NC	NC	NC	NC	NC
1-18	FLT3	NEG	BM	6219	NC	NC	NC	NC	NC	NC	NC	NC
1-19	FLT3	NEG	BM	5259	NC	NC	NC	NC	NC	NC	NC	NC
1-20	FLT3	NEG	BM	4443	NC	NC	NC	NC	NC	NC	NC	NC
1-21	FLT3	NEG	BM	5236	NC	NC	NC	NC	NC	NC	NC	NC
1-22	FLT3	NEG	BM	4443	NC	NC	NC	NC	NC	NC	NC	NC

BM bone marrow, CE capillary electrophoresis, DEL deletion, FFPE formalin-fixed paraffin-embedded, INS insertion, NC not called, NEG negative

ISSN: 1756-994X