Fig. 9
From: A simple procedure for directly obtaining haplotype sequences of diploid genomes
Data processing workflow. Fastq files are mapped to a reference with BWA to generate BAM files of aligned reads. ContigMetrics and TargetCut are used to generate scaffolds from the BAM files. GATK is used to generate VCF files. BuildRefHapinput takes VCF files and lists of scaffolds and outputs scaffold self consistency metrics and the input files for RefHap which is used to generate files of phased SNP using the SIH algorithm. ValidateSIHhaplotypes and validate haplotypes take haplotypes derived from SNP genotype data produced, e.g., with Beagle and compares them with haplotypes obtained by SIH and derived from scaffolds respectively