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