HaplotypeTools: a toolkit for accurately identifying recombination and recombinant genotypes

BMC Bioinformatics

Table 4 HaplotypeTools’ utility script HaplotypePlacer constructs haplotype trees with FastTree and identifies the closest relative to each

Lineage	BdAsia1	BdAsia2	BdCAPE	BdCH	BdGPL
HaplotypeCaller (nt)	2556	1637	5180	2418	7089
HaplotypeCaller (%)	14	9	27	13	38
HaplotypeTools (nt)	52,806	55,341	3,22,642	51,476	3,14,161
HaplotypeTools (%)	7	7	41	6	39
Whatshap (nt)	3,86,839	2,58,519	43,96,845	2,61,089	44,56,306
Whatshap (%)	4	3	45	3	46
Overlapping phase groups	889	940	1344	758	1018
Overlapping phased positions (OPP)	1941	2131	3457	1661	2487
OPP Same phase (nt)	1758	1922	3421	1486	2467
OPP Same phase (%)	91	90	99	89	99
OPP Cross-over (nt)	183	209	36	175	20
OPP Cross-over (%)	9	10	1	11	1

Hybrid Bd isolate SA-EC3 haplotypes from GATK v4 HaplotypeCaller physical phasing, HaplotypeTools and WhatsHap were analysed using HaplotypePlacer, finding that the majority of haplotypes from each of the three tools are closest in those trees to BdGPL (38–46%) and BdCAPE (27–45%). A HaplotypeTools utility script was used to compare phasing between SA-EC3 and each of the lineages. For each comparison, the script identified overlapping phase groups, comprising overlapping phased positions (OPP), which were either in the same phase, or showed evidence of crossovers

ISSN: 1471-2105