## sgcocaller: Calling crossovers from single-gamete DNA sequencing reads
Two main modules are available in `sgcocaller`, phasing and crossover calling.
`sgcocalelr phase` generate donor haplotype from single-gamete DNA sequencing data.
`sgcocaller phase` generates donor haplotype from single-gamete DNA sequencing data.
`sgcocaller xo` and `sgcocaller sxo` both call crossovers in each single
gamete using a Hidden Markov Model.
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## Inputs
- Bam, sorted and index bam file which contains DNA reads of single gamete cells
with `CB` tag, eg. from single-cell preprocessing pipeline (cellranger)
with `CB` tag, eg. from single-cell preprocessing pipeline (CellRanger, STARSolo, kallisto|bustools, alevin-fry, etc)
- VCF, variant call file that contains the list of informative SNPs (phased or unphased SNPs)
- barcodeFile, the list of cell barcodes of the gametes
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### Run for single-cell DNA sequenced gametes with donor haplotype known
In cases where the haplotype of the donors is known (i.e the list of hetSNPs have been phased, or the donor is F1 hybrid sample), `sgcocaller xo` can be called directly:
In cases where the haplotype of the donors is known (i.e the list of hetSNPs has been phased, or the donor is an F1 hybrid sample), `sgcocaller xo` can be called directly:
