jvarkit

VcfDistanceBetweenVariants

Annotate variants with the distance between previous and next variant.

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar vcfdistancevariants  [options] Files

Usage: vcfdistancevariants [options] Files
  Options:
    --bcf-output
      If this program writes a VCF to a file, The format is first guessed from 
      the file suffix. Otherwise, force BCF output. The current supported BCF 
      version is : 2.1 which is not compatible with bcftools/htslib (last 
      checked 2019-11-15)
      Default: false
    --generate-vcf-md5
      Generate MD5 checksum for VCF output.
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --out
      Output file. Optional . Default: stdout
    -p, --prefix
      INFO Attribute Prefix
      Default: DIST_
    --version
      print version and exit

Keywords

• vcf
• annotation
• distance

Creation Date

20190410

Source code

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

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/misc/VcfDistanceBetweenVariantsTest.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 vcfdistancevariants ? 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

$ java -jar dist/vcfdistancevariants.jar src/test/resources/toy.vcf.gz
##fileformat=VCFv4.2
##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
##INFO=<ID=DIST_NEXT,Number=1,Type=Integer,Description="Distance to next variant">
##INFO=<ID=DIST_PREV,Number=1,Type=Integer,Description="Distance to previous variant">
(..)
##contig=<ID=ref,length=45>
##contig=<ID=ref2,length=40>
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	S1
ref	11	.	A	C	0.52	.	AC1=1;AF1=0.498013;BQB=1;DIST_NEXT=3;DP=3;DP4=2,0,1,0;FQ=-6.97257;MQ=30;MQ0F=0;MQB=1;PV4=1,1,1,0.106148;RPB=1;SGB=-0.379885	GT:PL	0/1:21,0,46
ref	14	.	AG	AGGG	0.71	.	AC1=2;AF1=1;DIST_PREV=3;DP=3;DP4=0,0,1,0;FQ=-37.5301;IDV=2;IMF=0.666667;INDEL;MQ=30;MQ0F=0;SGB=-0.379885	GT:PL	0/1:30,3,0
ref2	14	.	C	T	0.09	.	AC1=1;AF1=0.487148;BQB=1;DIST_NEXT=0;DP=6;DP4=3,0,1,0;FQ=-14.1557;MQ=30;MQ0F=0;MQB=1;PV4=1,0,1,0.0285955;RPB=1;SGB=-0.379885	GT:PL	0/0:13,0,64
ref2	14	.	CAA	CAAATAA	32.43	.	AC1=2;AF1=1;DIST_NEXT=1;DIST_PREV=0;DP=6;DP4=0,0,3,0;FQ=-43.5253;IDV=1;IMF=0.166667;INDEL;MQ=30;MQ0F=0;SGB=-0.511536;VDB=0.354794	GT:PL	1/1:72,9,0
ref2	17	.	T	A	0.14	.	AC1=1;AF1=0.491968;BQB=1;DIST_PREV=1;DP=6;DP4=4,0,1,0;FQ=-12.2521;MQ=30;MQ0F=0;MQB=1;PV4=1,1,1,0.201057;RPB=1;SGB=-0.379885	GT:PL	0/0:15,0,72

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