`Program: sqtl (selection quantitative trait locus mapping)
Version: 0.1.3
Contact: Leopold Parts <leopold.parts@gmail.com>

Usage: sqtl <command> [options]

Command:
                map             Map fastq files to reference
                calc_afs        Create pileups at segregating sites, count reference and non-reference alleles, and infer allele frequencies
                    pileup          Create pileups at segregating sites
                    count           Count reference and non-reference alleles
                    infer           Infer posterior allele frequencies at segregating sites
                call_regions    Call regions with large change between pairs of samples

                plot_genome     Plot genome-wide allele frequencies
                plot_chrms      Plot allele frequencies separately for each chromosome
                plot_qtls       Plot allele frequencies at QTLs
      
                combine_count   Combine multiple count files
                combine_afs     Combine multiple allele frequency files
`