Usage: sga hapgen [OPTION] --ref REF.fa --sites SITES.txt READS.fa Generate candidate haplotypes around the SITES using the assembly graph of READS --help display this help and exit -v, --verbose display verbose output -r, --reference=FILE the reference genome to use -s, --sites=FILE the coordinates on the reference to generate haplotypes for -o, --outfile=FILE write results to FILE -k, --kmer=K use K as the k-mer size for variant discovery -x, --kmer-threshold=T only used kmers seen at least T times -t, --threads=NUM use NUM computation threads -d, --sample-rate=N use occurrence array sample rate of N in the FM-index. Higher values use significantly less memory at the cost of higher runtime. This value must be a power of 2 (default: 128) Report bugs to js18@sanger.ac.uk