A systematic evaluation of copy number alterations detection methods on real SNP array and deep sequencing data

BMC Bioinformatics

Table 2 Basic sequencing information and windows size estimation on 10 samples

Sample	Reads		Coverage (fold)		Ploidy	Window size (bp)
Sample	Tumor	Normal	Tumor	Normal	(ref)	CNVseq	FREEC	ReadDepth
357	1,891,204,418	1,947,625,118	61	63	2 (GPHMM)	1225	618	500
620,380	2,318,387,458	2,660,245,982	75	86	2 (GPHMM)	940	493	600
K2110056	1,665,457,542	1,614,695,950	54	52	2 (GPHMM)	1423	695	600
K2150024	1,468,032,864	1,821,106,022	47	59	2 (GPHMM)	1456	780	600
K2310007	1,707,025,098	1,534,828,476	55	50	2 (GPHMM)	1453	670	600
K2310024	1,795,611,576	1,914,189,016	58	62	2 (GPHMM)	1261	637	600
K2310030	1,565,239,138	1,552,514,106	51	50	2 (GPHMM)	1493	730	600
RS114527	1,750,239,946	1,406,561,492	57	45	4 (OncoSNP)	1517	655	600
K2110097	1,561,020,588	1,821,446,462	50	59	3 (GPHMM)	1725	740	600
K2150051	1,584,801,578	1,523,937,258	51	49	4 (GAP)	1509	726	600

ISSN: 1471-2105