From 1d9ba8f205d95f56dbce7cc3d754a868ef95e420 Mon Sep 17 00:00:00 2001
From: rlyu <rlyu@svi.edu.au>
Date: Mon, 11 Jan 2021 10:55:07 +1100
Subject: [PATCH] update readme

---
 README.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index ab6cf19..37df583 100644
--- a/README.md
+++ b/README.md
@@ -18,9 +18,11 @@ for deriving the inferred haplotype sequence against the list of SNP markers.
 ## Usage
 Obtain allele counts for cell barcodes listed in barcodeFile at the SNP positions in VCF from the BAM file.
 
+```
 Usage:
     sscocaller [options] <BAM> <VCF> <barcodeFile> <out_prefix>
 
+
 Options:
     -t --threads <threads> number of BAM decompression threads [default: 4]
     -MQ --minMAPQ <mapq> Minimum MAPQ for read filtering [default: 20]
@@ -36,4 +38,4 @@ Options:
 
 Examples
     ./sscocaller --threads 10 AAAGTAGCACGTCTCT-1.raw.bam AAAGTAGCACGTCTCT-1.raw.bam.dp3.alt.vcf.gz barcodeFile.tsv ./percell/ccsnp-
-
+```
-- 
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