A pipeline for sample tagging of whole genome bisulfite sequencing data using genotypes of whole genome sequencing

Table 1 Fingerprint panels that were investigated in this study

Fingerprint panel index	Origin/reference	Application of the panel	Number of variants	Number of autosomal variants	Number of autosomal variants captured by WGS of CNSR-III
1	Self-designed	DNA sample identification	52	52	52
2	Illumina HumanMethylation450 BeadChip array [20]	Sample identification for DNA methylation array	65	56	54
3	[21]	DNA sample identification	169	136	126
4	[13]	DNA sample identification and kinship analysis	448	336	321
5	[12]	DNA sample identification	1245	1218	1093
6	Affymetrix Genome-Wide Human SNP Array 6.0 [22]	Genotyping and chromosomal aberration analysis	929,867	890,404	756,584
7	Self-designed autosome-wide A/T polymorphic SNVs	Sample identification for WGBS	67107200^a	63881625^a	1309760^b
8	Self-designed autosomal A/T polymorphic common SNVs	Sample identification for WGBS	1351	1351	1351
9	Self-designed autosomal common SNVs	Sample identification for WGBS	1278	1278	1278

^a calculated using genetic variants data of dbSNP
^b filtered by the 200 bp bin where no CpG motif was found and ENCODE Blacklist of the human genome (see Methods)

ISSN: 1471-2164