From 23656862aa1362db004171f70e8e792aac986a62 Mon Sep 17 00:00:00 2001
From: rlyu <rlyu@svi.edu.au>
Date: Tue, 19 Jul 2022 12:31:51 +1000
Subject: [PATCH] update readme
---
README.md | 17 +++++++++--------
1 file changed, 9 insertions(+), 8 deletions(-)
diff --git a/README.md b/README.md
index 9869a16..5f34c61 100644
--- a/README.md
+++ b/README.md
@@ -31,17 +31,18 @@ with `CB` tag, eg. from single-cell preprocessing pipeline (CellRanger, STARSolo
- barcodeFile, the list of cell barcodes of the gametes
## Main outputs from sgcocaller phase
+
* *phased_snpAnnot.txt
- *_phased_snpAnnot.vcf.gz (if --outvcf)
- *_totalMtx.mtx
- *_altMtx.mtx
- *_gtMtx.mtx
+ * _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
+ * _corrected_phased_snpAnnot.txt
+ * _corrected_phased_snpAnnot.vcf.gz
+ * _switch_score.txt
## Main outputs from sgcocaller xo
@@ -121,7 +122,7 @@ Options:
./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