jvarkit

SamClipIndelFraction

Extract clipping/indel fraction from BAM

DEPRECATED

This tool can be replace with Bioalcidaejdk

Usage

Usage: Samclipindelfraction [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    --version
      print version and exit
    -t
      type
      Default: allclip
      Possible Values: [leftclip, rightclip, allclip, insert, deletion]

Keywords

• sam
• bam
• clip

Compilation

Requirements / Dependencies

• java compiler SDK 11. Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew Samclipindelfraction

The java jar file will be installed in the dist directory.

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/misc/SamClipIndelFraction.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/misc/SamClipIndelFractionTest.java

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues
• Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite Samclipindelfraction ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

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,])

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