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

BMC Genomic Data

Table 5 Input files of 6 HA algorithms as stated in their papers or user manuals

Method	VCF	BAM	Matrix	Input
HapCUT2	X	X		Haplotype fragments (BAM files) and a list of heterozygous variants (VCF)
MixSIH				Aligned SNP fragments
PEATH			X	Two n by m matrices: M and Q (M = sequence read matrix; Q = quality score matrix)
WhatsHap	X	X		VCF file with variants of an individual and a BAM file with sequencing reads from that same individual
SDhaP			X	Reads were arranged into an m by n matrix according to positions on chromosome
MAtCHap			X	Uses one n by m fragment matrix where each row (n) represents reads and each column (m) represents the information of a heterozygous variant

The columns (from left to right) are HA methods, commonly used input formats (VCF file, BAM file, and Matrix), and input description. Each “X” represents the input format(s) that the given software package uses. The last column is a more detailed description of different input formats used in each algorithm

ISSN: 2730-6844