`sscocaller` processes DNA reads from each single sperm in the aligned and sorted BAM file for detecting crossovers by identifying haplotype shifts. It takes the large bam file which contains aligned DNA reads from a list of single sperm cells and summarizes allele counts for the provided informative SNP markers. A HMM model is applied for haplotyping each sperm and viterbi algorithm is run for deriving the inferred haplotype sequence against the list of SNP markers.
