From 23f45782a25fac277f442bc1632bf757bdc70524 Mon Sep 17 00:00:00 2001
From: Ruqian Lyu <rlyu@svi.edu.au>
Date: Thu, 22 Jul 2021 01:12:58 +0000
Subject: [PATCH] Update README.md
---
README.md | 22 +++++++++++-----------
1 file changed, 11 insertions(+), 11 deletions(-)
diff --git a/README.md b/README.md
index bc25e60..d8740a5 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
--
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