sgcocaller xo [options] <BAM> <VCF> <barcodeFile> <out_prefix>
Arguments:
<BAM> the read alignment file with records of single-cell DNA reads
<VCF> the variant call file with records of SNPs with hetSNPs phased in the form of REF/ALT or the GT field
<VCF> the variant call file with records of SNPs
<barcodeFile> the text file containing the list of cell barcodes
<out_prefix> the prefix of output files
<out_vcf> the output vcf aftering phasing blocks in hapfile
<gtMtxFile> the output gtMtx.mtx file from running sgcocaller phase
<phasedSnpAnnotFile> the output phased_snpAnnot.txt from running sgcocaller phase
Options:
-t --threads <threads> number of BAM decompression threads [default: 4]
--barcodeTag <barcodeTag> the cell barcode tag in BAM [default: CB]
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@@ -78,22 +99,29 @@ Options:
--thetaALT <thetaALT> the theta for the binomial distribution conditioning on hidden state being ALT [default: 0.9]
--cmPmb <cmPmb> the average centiMorgan distances per megabases default 0.1 cm per Mb [default: 0.1]
--phased the input VCF for calling crossovers contains the phased GT of heterozygous SNPs
--outvcf generate the output in vcf format (phase)
--outvcf generate the output in vcf format (sgcocaller phase)
--templateCell <templateCell> the cell's genotype to be used a template cell, as the cell's index (0-starting) in the barcode file, default as not supplied [default: -1]
--maxDissim <maxDissim> the maximum dissimilarity for a pair of cell to be selected as potential template cells due to not having crossovers in either cell [default: 0.0099]
--maxExpand <maxExpand> the maximum number of iterations to look for locally coexisting positions for inferring missing SNPs in template haplotype sequence [default: 1000]
--posteriorProbMin <posteriorProbMin> the min posterior probability when inferring missing SNPs [default: 0.99]
--posteriorProbMin <posteriorProbMin> the min posterior probability for inferring missing SNPs [default: 0.99]
--lookBeyondSnps <lookBeyondSnps> the number of local SNPs to use when finding switch positions [default: 25]
--minSwitchScore <minSwitchScore> the minimum switch score for a site to be identified as having a switch error in the inferred haplotype and corrected [default: 50.0]
--minPositiveSwitchScores <minPositiveSwitchScores> the min number of continuing SNPs with positive switch scores to do switch error correction [default: 8]
--minSwitchScore <minSwitchScore> the minimum switch score for a site to be identified as having a switch error in the inferred haplotype [default: 50.0]
--minPositiveSwitchScores <minPositiveSwitchScores> the min number of continuing SNPs with positive switch scores to do switch error correction [default: 8]
--binSize <binSize> the size of SNP bins for scanning swith errors, users are recommended to increase this option when SNP density is high. [default: 2000]
--stepSize <stepSize> the move step size used in combination with --binSize. [default: 200]
--dissimThresh <dissimThresh> the threshold used on the allele concordance ratio for determining if a SNP bin contains a crossover. [default: 0.0099]
--batchSize <batchSize> the number of cells to process in one batch when running sxo. This option is only needed when the memory is limited.
--notSortMtx do not sort the output mtx.
--maxUseNcells <maxUseNcells> the number of cells to use for calculating switch scores. All cells are used if not set
