From 79aa70cc08590cb6f642eff51968d6da36330a2c Mon Sep 17 00:00:00 2001
From: rlyu <rlyu@svi.edu.au>
Date: Tue, 19 Jul 2022 12:27:41 +1000
Subject: [PATCH] update read me
---
README.md | 56 +++++++++++++++++++++++++++++++++++++++++--------------
1 file changed, 42 insertions(+), 14 deletions(-)
diff --git a/README.md b/README.md
index 2a7c76b..9869a16 100644
--- a/README.md
+++ b/README.md
@@ -30,7 +30,20 @@ with `CB` tag, eg. from single-cell preprocessing pipeline (CellRanger, STARSolo
- VCF, variant call file that contains the list of informative SNPs (phased or unphased SNPs)
- barcodeFile, the list of cell barcodes of the gametes
-## Main outputs
+## Main outputs from sgcocaller phase
+* *phased_snpAnnot.txt
+ *_phased_snpAnnot.vcf.gz (if --outvcf)
+ *_totalMtx.mtx
+ *_altMtx.mtx
+ *_gtMtx.mtx
+
+## Main outputs from sgcocaller swphase (or sgcocaller autophase)
+* *cellGenoVersusTemplate.txt
+ *_corrected_phased_snpAnnot.txt
+ *_corrected_phased_snpAnnot.vcf.gz
+ *_switch_score.txt
+
+## Main outputs from sgcocaller xo
* *.mtx
* sparse matrix with columns corresponding to the list of gamete cell barcodes and rows corresponding to the list of SNP positions in VCF file
@@ -47,22 +60,30 @@ with `CB` tag, eg. from single-cell preprocessing pipeline (CellRanger, STARSolo
```
-Usage:
- sgcocaller phase [options] <BAM> <VCF> <barcodeFile> <out_prefix>
- sgcocaller swphase [options] <gtMtxFile> <phasedSnpAnnotFile> <referenceVCF> <out_prefix>
+ Usage:
+ sgcocaller autophase [options] <BAM> <VCF> <barcodeFile> <out_prefix>
+ sgcocaller phase [options] <BAM> <VCF> <barcodeFile> <out_prefix>
+ sgcocaller swphase [options] <gtMtxFile> <phasedSnpAnnotFile> <referenceVCF> <out_prefix>
sgcocaller sxo [options] <SNPPhaseFile> <phaseOutputPrefix> <barcodeFile> <out_prefix>
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]
@@ -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
-h --help show help
Examples
- ./sgcocaller phase --threads 4 --barcodeTag CB --chrom 'chr1' --minDP 2 possorted_bam hetSNPs.vcf.gz barcodeFile.txt outdir/path/withPrefix_
- ./sgcocaller xo --threads 4 possorted_bam.bam dbSNP-hetSNPs.vcf.gz barcodeFile.tsv ./percell/ccsnp
- ./sgcocaller sxo phaseOutputPrefix barcodeFile.tsv ./percell/ccsnp
-
+ ./sgcocaller autophase possorted_bam.bam hetSNPs.vcf.gz barcodeFile.tsv phaseOutputPrefix
+ ./sgcocaller phase possorted_bam.bam hetSNPs.vcf.gz barcodeFile.tsv phaseOutputPrefix
+ ./sgcocaller xo --threads 4 possorted_bam.bam phased_hetSNPs.vcf.gz barcodeFile.tsv ./percell/ccsnp
+ ./sgcocaller sxo snp_phase.txt phaseOutputPrefix barcodeFile.tsv ./percell/ccsnp
+
```
### Run for single-cell DNA sequenced gametes with donor haplotype known
--
GitLab