Update README.md

Author: Akanksha2511

README.md

@@ -106,6 +106,7 @@ Optional arguments:
 | -sin --singlechrom			     | False         | parallel code for single chromosome; *npp* will be used for parallel run for each chr
 | -d --delta			             | 0.1     	     | minimum average difference in methylation required in a DMR 
 | -wrt --withrespectto		    | all     	     | samples to use for DMR calling for pairwise comparisions with respect to specific samples
+| -Keepall --Keepall		      | False     	   | Keep all cytosine positions present in atleast one of the replicate
 
 **Parameter –sc**
 
@@ -162,6 +163,11 @@ This parameter is used if you want to select the samples from anywhere in your s
 
 This parameter is used if you want to provide CGmap file directly. The default is False, so the code will require the files in the input format mentioned above. If the user have methyaltion output files from BSSeeker2, it can be provided directly. To turn it on just say *-BSSeeker2* in the command line. 
 
+
+**Parameter –Keepall**
+
+This parameter is used if you want keep all the positions present in any of the replicates. The default is False, so it will keep only those position that are present in all the replicates of a sample. This parameter is especially useful if the dataset contains more than 1 replicate and contains missing positions which are coverged in atleast one of the replicate. To turn it on just say *-Keepall* in the command line. 
+
 **Parameter –wrt**
 
 This parameter is used if user want to run multiple parawise comparsions with recpect to only specific samples, instead of for all pairwise combinations. For example if user want to compare control (cnt) with all other samples, he/she can use below command:
@@ -215,7 +221,7 @@ Optional arguments:
 | -mc --minc			             | 4 	           | minimum number of Cs in a DMR
 | -d --delta			             | 0.1     	     | minimum average difference in methylation required in a DMR
 | -sin --singlechrom			     | False         | parallel code for single chromosome; *npp* will be used for parallel run for each chr
-
+| -Keepall --Keepall		      | False     	   | Keep all cytosine positions present in atleast one of the replicate
 
 **Output format**