README.md

README.md

@@ -18,7 +18,7 @@ choppy install YaqingLiu/CNVkit
 ```
 
 ## Copy number calling pipeline
-![image](https://cnvkit.readthedocs.io/en/stable/_images/workflow.png)
+<img src="https://cnvkit.readthedocs.io/en/stable/_images/workflow.png" div align=center/>
 
 ## Input
 ```json
@@ -49,30 +49,32 @@ choppy install YaqingLiu/CNVkit
 }
 ```
 **Note**
-*-m {hybrid,amplicon,wgs}, --seq-method {hybrid,amplicon,wgs}, --method {hybrid,amplicon,wgs}*
+
+***-m {hybrid,amplicon,wgs}, --seq-method {hybrid,amplicon,wgs}, --method {hybrid,amplicon,wgs}***
 
 Sequencing assay type: hybridization capture ('hybrid'), targeted amplicon sequencing ('amplicon'), or whole genome sequencing ('wgs').
 Determines whether and how to use antitarget bins.
 
 To reuse an existing reference or create a new :
 
-*-r REFERENCE, --reference REFERENCE*
+***-r REFERENCE, --reference REFERENCE***
 
 Copy number reference file (.cnn).
 
-*--output-reference FILENAME*
+***--output-reference FILENAME***
 
 Output filename/path for the new reference file being created. (If given, ignores the -o/--output-dir option and will write the file to the given path. Otherwise, "reference.cnn" will be created in the current directory or specified output directory.)
 
-*--annotate*
+***--annotate***
 
 The gene annotations file (refFlat.txt) is useful to apply gene names to your baits BED file, if the BED file does not already have short, informative names for each bait interval. This file can be used in the next step.
 If the BED looks like this:
-> chr1	1508981	1509154	SSU72
+> chr1   1508981   1509154   SSU72
 > 
-> chr1  2407978 2408183 PLCH2
+> chr1   2407978   2408183   PLCH2
 > 
-> chr1  2409866 2410095 PLCH2
+> chr1   2409866   2410095   PLCH2
+
 Then you don’t need refFlat.txt.
 
 ## Output