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