SamClipIndelFraction

##Motivation

Extract clipping/indel fraction from BAM

##Compilation

See also Compilation.

$  ant samclipindelfraction

##Synopsis

$ java -jar dist/samclipindelfraction.jar [option] (stdin|file.bam) 

##Options

Option	Description
-t (type)	one of: [leftclip, rightclip, allclip, insert, deletion]
-h	get help (this screen) and exit.
-v	print version and exit.
-L (level)	log level. One of java.util.logging.Level . Optional.
--doap	prints a DOAP+XML description of the program and exit

##Source Code

Main code is: https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/misc/SamClipIndelFraction.java

##Example

$ samtools view -h -F3844 my.bam  | java -jar dist/samclipindelfraction.jar 

##UNMAPPED_READS=0
##MAPPED_READS=3028359
##CLIPPED_READS=1182730
##CLIPPED_READS_5_PRIME=597757
##CLIPPED_READS_3_PRIME=617399
##UNCLIPPED_READS=1845629
##COUNT_BASES=338644685
#CLIP	COUNT	FRACTION_OF_MAPPED_READS
0	1845629	0.5
1	7	1.8963724562195327E-6
2	6756	0.0018302703306027376
3	695	1.8828269386751074E-4
4	794	2.1510281860547272E-4
5	819	2.2187557737768533E-4
6	471	1.275987752684857E-4
7	447	1.210969268471616E-4
(...)

plotting:

$ java -jar dist/samclipindelfraction.jar |\
   grep -v "##" | cut -f1,2 | tr -d '#' > output.txt

then, in R:

T<-read.table('output.txt',header=TRUE)
plot(T[T$CLIP>0,])

##See also

##History

• 2014: Creation