STR-realigner: a realignment method for short tandem repeat regions

BMC Genomics

Table 13 The numbers of estimated repeat numbers matched and mismatched with parents in terms of Mendelian inheritance

Period	STR-realigner		ReviSTER		IndelRealigner		Original BAM
	#CR	#IR	#CR	#IR	#CR	#IR	#CR	#IR
1	1305	533	1319	540	1314	531	1298	531
	(1,416)	(563)
2	280	82	269	80	242	90	242	87
3	63	5	56	7	56	6	57	5
4	196	28	183	34	169	38	169	33
5	41	15	46	18	44	16	44	15
6	35	9	34	12	33	13	33	13
Total	1920	672	1907	691	1858	694	1843	684

The number of consistent regions (#CR), and the number of inconsistent regions (#IR) based on estimated repeat numbers with RepeatSeq in a parent-offspring trio, NA12878, NA12891 and NA19892, for the original BAM files, those realigned with STR-realigner, ReviSTER, and GATK IndelRealigner are summarized. Values in parentheses for STR-realigner are the result without filtering long homopolymer regions. The best result is underlined

ISSN: 1471-2164