Pairwise comparative analysis of six haplotype assembly methods based on users’ experience

BMC Genomic Data

Table 8 Block and SNV number summary of the hg19 and hg38 DP1 data

hg19.DP1.no.HI	filterSNV (no”-“)	Block (no “-“)	Min	Q1	Median	Mean	Q3	Max
HapCUT2	115,215	32,150	2	2	2	3.58	4	770
MixSIH	115,790	32,252	2	2	2	3.59	4	770
PEATH	115,813	31,355	2	2	2	3.69	4	770
WhatsHap	178,523	10,132	2	2	2	17.6	9	5194
SDhaP	115,813	32,252	2	2	2	3.59	4	770
MAtCHap	115,813	31,355	2	2	2	3.69	4	770
hg38 DP1.no.HI	filterSNV (no”-“)	Block (no “-“)	Min	Q1	Median	Mean	Q3	Max
HapCUT2	100,686	21,710	2	2	2	4.64	5	2187
MixSIH	100,807	21,726	2	2	3	4.64	5	2190
PEATH	100,810	19,660	2	2	3	5.13	4	6988
WhatsHap	100,785	21,654	2	2	3	4.65	5	2479
SDhaP	100,810	21,726	2	2	3	4.64	5	2190
MAtCHap	100,810	19,660	2	2	3	5.13	4	6988

The top 7 rows are for the hg19 DP1 data. The bottom 7 rows are for the hg38 DP1 data. The first 3 columns are the HA names, total number of SNVs (after “-” being removed), and total number of haplotype blocks. “no.HI” in the first column means that homozygous variants and indel sites were not included. Columns 4 to 9 show a summary of the number of SNVs per block for all blocks listed in the third column. “Min” means minimum. “Max” means maximum. “Q1” is the 25th percentile. “Q3” is the 75th percentile

ISSN: 2730-6844