diff --git a/README.md b/README.md index db2341a39b03cb4dbbbccf7ec704827b9df80c84..7a69864a7956665bf6a651d874d44ac4af9fe610 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ ## 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. @@ -22,7 +22,7 @@ sequence for the list of SNP markers. ## 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 @@ -98,7 +98,7 @@ Options: ``` ### 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: For F1 hybrid donor: