updated documentation

docs/README.md

@@ -69,7 +69,7 @@ If no options are used the help menu will appear.
   				[-inputDir, -outputDir, -bed, -controlsDir]
   				OPTIONAL:
   				[-rmDup, -useSampleAsControl]
-  			StartWithAvgCount :
+  			  			StartWithAvgCount :
   				Start with Average Count files as input. This is a five column text file
   				with predefined column names. Please read the manual for instructions.
   				REQUIRED:
@@ -110,7 +110,7 @@ If no options are used the help menu will appear.
   -controlSamples       Number of samples to use in Match score analysis. DEFAULT: 30
   -regionThreshold      Percentage of all control samples differing more than 3
                         standard deviations from mean coverage of a region in the specified
-                        BED file to exlude from sample ratio calculation. DEFAULT: 20
+                        BED file to exlude from sample CV calculation. DEFAULT: 20
   -rmDup                Switch to enable duplicate removal when using BAM files as input.
   -sexChr               Switch to include sex chromosomes in analysis.
   -useSampleAsControl   Switch to use samples as control. Example: when using BAM
@@ -124,8 +124,8 @@ If no options are used the help menu will appear.
                         this threshold are marked as deletion. DEFAULT: -3
   -zScoreCutOffHigh     Higher Z-score cutoff value. Regions with a Z-score above
                         this threshold are marked as duplication. DEFAULT: 3
-  -sampleRatioScore     Sample ratio z-score cutoff value. Sample with a ratio
-                        score below this value are excluded from analysis. DEFAULT: 0.09
+  -sampleRatioScore     Sample CV z-score cutoff value. Sample with a ratio
+                        score below this value are excluded from analysis. DEFAULT: 0.09. NOTE: this variable now is named "SAMPLE CV" in all outputs!
   -percentageLessReliableTargets	Target labelled as less reliable in percentage
                         of control samples. DEFAULT: 20
 ```
@@ -334,10 +334,11 @@ To apply a threshold of ratio score below 0.65 for a deletion and above 1.4 for
 The same thresholds for calling a deletion or duplication can also be applied using the Z-score value cutoff.
 To call a deletion when the Z-score is below -3 or duplication when the Z-score is above 3 use:
 ```bash
-  -zScoreCutOffLow -3
+  -zScoreCutOffLow=-3
   -zScoreCutOffHigh 3
 ```
 
+Note that to use the minus variable in the -zScoreCutOffLow an '=' sign is needed instead of a space.
 
 To finetune the variant list one can generate a list of targets which in general are of lower quality in all possible controlsamples and apply this as a filter to generate a final list of high quality calls. This can be done by executing two steps:
 
@@ -375,7 +376,6 @@ This produces the following output file:
 *.finallist.txt* contains all final calls, basically a filtered shortlist file.
 
 
-
 # Test dataset
 
 A test dataset can be downloaded from [here](https://github.com/molgenis/CoNVaDING/tree/master/Test_dataset).
@@ -501,15 +501,15 @@ The totallist contains the information of all targets and shows the ratio's and
 *Sample1.average.counts.best.score.totallist.txt*
 ```bash
   CHR	START	   STOP	       GENE	  .. .. AUTO_VC     .. .. .. ABBERATION   QUALITY
-  1     156104958  156105124  LMNA	  .. .. 0.06058213  .. .. .. DEL          .
+  1     156104958   156105124  LMNA	  .. .. 0.06058213  .. .. .. DEL          .
   ..						
-  2     179511192  179511307  TTN	  .. .. 0.095184824 .. .. .. DEL          .
+  2     179511192   179511307  TTN	  .. .. 0.095184824 .. .. .. DEL          .
   ..
   6     7576507	   7576710	  DSP	  .. .. 0.051947043 .. .. .. DUP          .
-  6	    7577172	   7577296	  DSP	  .. .. 0.094469481 .. .. .. DUP          . 
-  6	    7577992	   7578140	  DSP	  .. .. 0.061275822 .. .. .. DUP          .
+  6	   7577172	  7577296   DSP	  .. .. 0.094469481 .. .. .. DUP          . 
+  6	   7577992	  7578140   DSP	  .. .. 0.061275822 .. .. .. DUP          .
   ..						
-  12    21997397   21997507	  ABCC9   .. .. 0.120684521 .. .. .. DUP          LOW_QUALITY
+  12    21997397   21997507   ABCC9   .. .. 0.120684521 .. .. .. DUP         LOW_QUALITY
   ..						
   18    28647961   28648199   DSC2	  .. .. 0.063042636 .. .. .. DEL          .
   18    28648255   28648331   DSC2	  .. .. 0.160488643 .. .. .. DEL          LOW_QUALITY
@@ -603,7 +603,6 @@ Sample CV: 0.09
 Target CV: 0.10
 
 
-
 #FAQ
 
 Which are the criteria of adding a call to the longlist, shortlist or finallist?
@@ -635,12 +634,30 @@ All the targets on the X chromosome are of low quality.
 
 - Make sure all control samples are of the same gender. 
 
+When settig the -zScoreCutOffLow parameter on X I get 'Unknown option :X'
+
+- If the parameteres in the print to the screen are set correctly the output is correct. However, to prevent the error message instead of a space use an = sign to connect the variable. For instance:\
+
+```
+-zScoreCutOffLow=-3
+```
+
+
 
 
 
-# Changelog v1.2.0
+# Changelog
 The following bugs have been fixed in the update from version 1.1.6 to v1.2.0:
 
+
+##v1.2.1
+- Enabled merging HOM_DEL/HOM_DUP and DEL/DUP calls. Now everything works correctly.  
+
+##v1.2.0.1
+- Disabled merging HOM_DEL/HOM_DUP and DEL/DUP calls as implemented in v1.2.0, because of a bug resulting in showing the start position of the last exon in the call in the longlist instead of the first exon in the call.
+
+##v1.2.0
+
 ###Major
 - In version 1.1.6 after running the StartWithBam function analyzing a region having a coverage of 0, the normalized coverage would have a value of -NaN. This issue is fixed in version 1.2.0, by adding the -a flag to the samtools depth function. However, this causes a dependency on samtools version 1.3 or higher. 
 - In version 1.1.6 HOM_DEL and HOM_DUP calls were interpreted as separate events as DEL and DUP calls. This could cause calls to be cut into several pieces and create gaps in the calls because of downstream filtering. Now, HOM_DEL calls are interpreted as part of a DEL call as well as a separate call. For instance if exons 1 and 3 have a DEL call in the totallist and exon 2 a HOM_DEL call. A deletion of exons 1 to 3 will be called as well as a homozygous deletion of exon 2. Similarly HOM_DUP events are considered as part of DUP events as well as a separate call. Note that in case all targets of a call are considered HOM_DEL or HOM_DUP the call will appear twice on the longlist, shortlist and/or finallist.

docs/SUMMARY.md

@@ -9,7 +9,7 @@
 	* [Test dataset](./README.md#test-dataset)
 	* [QC Thresholds](./README.md#qc-thresholds)
 	* [FAQ](./README.md#faq)
-	* [Changelog](./README.md#changelog-v1.2.0)
+	* [Changelog](./README.md#changelog)
 	* [Literature](./README.md#literature)
 	* [Tutorial](./README.md#tutorial)
 	* [Contact](./README.md#contact)