`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.
[sscocaller_fig](images/sscocaller_fig.png)
## Inputs
- Bam, sorted and index bam file which contains DNA reads of single sperm cells with CB tag, eg. from single-cell alignment pipeline (cellranger)
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## Outputs
-*.mtx
- sparse matrix with columns corresponding to the list of sperm cell barcodes and rows corresponding to the list of SNP positions in VCF file
- {sample}_chr1_altCount.mtx, a sparse mtx with entries representing alternative allele counts
- {sample}_chr1_totalCount.mtx, a sparse mtx with entries representing total allele counts
- {sample}_chr1_vi.mtx, a sparse mtx with entries representing inferred viterbi state (haplotype state)
- {sample}_chr1_snpAnnot.txt, the SNP positions and allele
- {sample}_chr1_SegInfo.txt, statistics of viterbi state segments in text file format. It contains consecutive viterbi states for each chromosome with statistics including, starting SNP position, ending SNP position, the number of SNPs supporting the segment, the log likelihood ratio of the viterbi segment and the inferred hidden state.
**.mtx
* sparse matrix with columns corresponding to the list of sperm cell barcodes and rows corresponding to the list of SNP positions in VCF file
* {sample}_chr1_altCount.mtx, a sparse mtx with entries representing alternative allele counts
* {sample}_chr1_totalCount.mtx, a sparse mtx with entries representing total allele counts
* {sample}_chr1_vi.mtx, a sparse mtx with entries representing inferred viterbi state (haplotype state)
* {sample}_chr1_snpAnnot.txt, the SNP positions and allele
* {sample}_chr1_SegInfo.txt, statistics of viterbi state segments in text file format. It contains consecutive viterbi states for each chromosome with statistics including, starting SNP position, ending SNP position, the number of SNPs supporting the segment, the log likelihood ratio of the viterbi segment and the inferred hidden state.
