Changes between Version 40 and Version 41 of SOPs/miningSAMBAM

Timestamp:

08/31/18 14:53:24 (7 years ago)

Author:

ibarrasa

Comment:

--

SOPs/miningSAMBAM

@@ -136 +136 @@
 }}}
 
+=== Remove or mark duplicate reads in bam files ===
+
+{{{
+# Using picard tools, mark duplicates only, this is the default
+/pathtojava/java -jar /path_to_picard-tools/picard.jar  MarkDuplicates  I=input.bam O=ouput.marked_duplicates.bam \
+      M=ouputFileWithStats_metrics.txt  REMOVE_DUPLICATES=FALSE
+
+
+# Using picard tools, remove duplicates
+/pathtojava/java -jar /path_to_picard-tools/picard.jar  MarkDuplicates  I=input.bam O=ouput.marked_duplicates.bam \
+      M=ouputFileWithStats_metrics.txt  REMOVE_DUPLICATES=TRUE
+          
+}}}
+
 
 === View alignment with samtools ===