Update: README.md

README.md

@@ -1,28 +1,21 @@
-#### Introduction
 This APP developed for somatic short variant discovery (SNVs + Indels).
 
-Supported callers:
+**Supported callers**
 * TNhaplotyper2
 * TNscope
 * VarScan
 * TNhaplotyper (This caller is only available in `v0.1.0` as it is too outdated)
 Variant caller can be selected by setting `ture/false` in the submitted sample.csv.
 
-Types of data that can be received:
+**Types of data that can be received**
 * TN matched WES
 * WGS
 The datatype is judged by whether the bed file is set (i.e. the `regions` in inputs).
 
-**New version**
+#### New version
 * The TNhaplotyper, also named as TNseq in `v0.1.0`, has beed substituted by TNhaplotyper2.
 * The `corealigner` step has been removed.
 
-**Please carefully check**
-* the reference genome
-* bed file
-* the caller you want to use
-* whether PoN needs to be set
-
 #### How to run this APP
 
 We recommend using choppy system and Aliyun OSS service. The command will look like this:
@@ -41,7 +34,11 @@ choppy batch YaqingLiu/variant-calling-latest samples.csv -p Project -l Label
 choppy query -L Label | grep "status"
 ```
 
-**Please note**
-The `defaults` can be forcibly replaced by the settings in `samples.csv`.
+**Please note**: The `defaults` can be forcibly replaced by the settings in `samples.csv`. Therefore, there is no need to contact me over this issue.
 
-Therefore, there is no need to contact me over this issue.
+
+**Please carefully check**
+* the reference genome
+* bed file
+* the caller you want to use
+* whether PoN needs to be set