diff --git a/README.md b/README.md
index bc25e608d0e4cffd881583957c475bca61462602..d8740a5d7ac5605ed8a21156624b660c42a2ea6a 100644
--- a/README.md
+++ b/README.md
@@ -42,17 +42,17 @@ with `CB` tag, eg. from single-cell preprocessing pipeline (cellranger)
 
   Options:
       -t --threads <threads> number of BAM decompression threads [default: 4]
-      -MQ --minMAPQ <mapq> Minimum MAPQ for read filtering [default: 20]
-      -BQ --baseq <baseq>  base quality threshold for a base to be used for counting [default: 13]
-      -CHR --chrom <chrom> the selected chromsome (whole genome if not supplied,separate by comma if multiple chroms)
-      -minDP --minDP <minDP> the minimum DP for a SNP to be included in the output file [default: 1]
-      -maxDP --maxDP <maxDP> the maximum DP for a SNP to be included in the output file [default: 5]
-      -maxTotalDP --maxTotalDP <maxTotalDP> the maximum DP across all barcodes for a SNP to be included in the output file [default: 25]
-      -minTotalDP --minTotalDP <minTotalDP> the minimum DP across all barcodes for a SNP to be included in the output file [default: 10]
-      -chrName --chrName <chrName> the chr names with chr prefix or not, if not supplied then no prefix
-      -thetaREF --thetaREF <thetaREF> the theta for the binomial distribution conditioning on hidden state being REF [default: 0.1]
-      -thetaALT --thetaALT <thetaALT> the theta for the binomial distribution conditioning on hidden state being ALT [default: 0.9]
-      -cmPmb --cmPmb <cmPmb> the average centiMorgan distances per megabases default 0.1 cm per Mb [default 0.1]
+      --minMAPQ <mapq> Minimum MAPQ for read filtering [default: 20]
+      --baseq <baseq>  base quality threshold for a base to be used for counting [default: 13]
+      --chrom <chrom> the selected chromsome (whole genome if not supplied,separate by comma if multiple chroms)
+      --minDP <minDP> the minimum DP for a SNP to be included in the output file [default: 1]
+      --maxDP <maxDP> the maximum DP for a SNP to be included in the output file [default: 5]
+      --maxTotalDP <maxTotalDP> the maximum DP across all barcodes for a SNP to be included in the output file [default: 25]
+      --minTotalDP <minTotalDP> the minimum DP across all barcodes for a SNP to be included in the output file [default: 10]
+      --chrName <chrName> the chr names with chr prefix or not, if not supplied then no prefix
+      --thetaREF <thetaREF> the theta for the binomial distribution conditioning on hidden state being REF [default: 0.1]
+      --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]
       -h --help  show help
 
   Examples