VcfRebase

Last commit

Restriction sites overlaping variations in a vcf

Usage

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

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

Usage: vcfrebase [options] Files
  Options:
    -A, --attribute
      VCF INFO attribute
      Default: ENZ
    --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
    -E, -enzyme, --enzyme
      restrict to that enzyme name. Default: use all enzymes
      Default: []
    --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
    -R, -reference, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict
    --version
      print version and exit
    -w, -weight, --weight
      min enzyme weight 6 = 6 cutter like GAATTC, 2 = 2 cutter like ATNNNNNNAT
      Default: 5.0

Keywords

vcf
rebase
restriction
enzyme

Creation Date

20131115

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfrebase/VcfRebase.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/vcfrebase/VcfRebaseTest.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 vcfrebase ? 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/vcfrebase.jar -w 6 -R ~/data/human_g1k_v37.fasta src/test/resources/test_vcf01.vcf | bcftools annotate -x '^INFO/ENZ' | bcftools view --drop-genotypes | grep ENZ

##INFO=<ID=ENZ,Number=.,Type=String,Description="Enzyme overlapping: Format: (Name|Site|Sequence|pos|strand)">
##bcftools_annotateCommand=annotate -x ^INFO/ENZ; Date=Wed Nov 13 10:38:39 2019
1   852063  .   G   A   387 PASS    ENZ=PflMI|CCANNNN^NTGG|CCAGGCCCTGG|852064|+
1   866893  .   T   C   431 PASS    ENZ=SacI|GAGCT^C|GAGCtC|866889|+
1   875770  .   A   G   338 PASS    ENZ=ClaI|AT^CGAT|ATCGaT|875766|+
1   909238  .   G   C   229 PASS    ENZ=PmaCI|CAC^GTG|CACgTG|909235|+
1   913889  .   G   A   372 PASS    ENZ=BsaXI|(9/12)ACNNNNNCTCC(10/7)|GGAGGCCCCgT|913880|-
1   918384  .   G   T   489 PASS    ENZ=DraIII|CACNNN^GTG|CACgCCGTG|918381|+
1   933790  .   G   A   436 PASS    ENZ=BsaXI|(9/12)ACNNNNNCTCC(10/7)|GGAGGAGGGgT|933781|-
1   940005  .   A   G   188 PASS    ENZ=GsuI|CTGGAG(16/14)|CTGGAG|940006|+,BaeI|(10/15)ACNNNNGTAYC(12/7)|GGTaCTGGAGT|940002|-
1   940096  .   C   T   487 PASS    ENZ=BcgI|(10/12)CGANNNNNNTGC(12/10)|cGAGGTGGGTGC|940096|+
1   950113  .   GAAGT   G   1427    PASS    ENZ=Eco57I|CTGAAG(16/14)|CTgaag|950111|+
1   950243  .   A   C   182 PASS    ENZ=BclI|T^GATCA|TGaTCA|950241|+
1   951283  .   C   T   395 PASS    ENZ=NarI|GG^CGCC|GGcGCC|951281|+
1   951564  .   A   G   105 PASS    ENZ=BstXI|CCANNNNN^NTGG|CCaAGTAGTTGG|951562|+
1   952003  .   G   A   177 PASS    ENZ=Bpu10I|CCTNAGC(-5/-2)|CCTCAGC|952004|+,BbvCI|CCTCAGC(-5/-2)|CCTCAGC|952004|+
1   952428  .   G   A   456 PASS    ENZ=EciI|GGCGGA(11/9)|TCCgCC|952425|-
1   953952  .   G   A   490 PASS    ENZ=BsrDI|GCAATG(2/0)|CATTgC|953948|-
1   959155  .   G   A   370 PASS    ENZ=BarI|(7/12)GAAGNNNNNNTAC(12/7)|gAAGCCGCTCTAC|959155|+
1   959231  .   G   A   350 PASS    ENZ=BsaXI|(9/12)ACNNNNNCTCC(10/7)|GGAGGGTCCgT|959222|-
1   960409  .   G   C   357 PASS    ENZ=BseYI|CCCAGC(-5/-1)|CCCAgC|960405|+
1   962210  .   A   G   300 PASS    ENZ=NcoI|C^CATGG|CCaTGG|962208|+
1   964389  .   C   T   32  LowGQXHetSNP;LowGQXHomSNP   ENZ=BseYI|CCCAGC(-5/-1)|cCCAGC|964389|+
1   967658  .   C   T   515 PASS    ENZ=StuI|AGG^CCT|AGGCcT|967654|+
1   970215  .   G   C   379 PASS    ENZ=DrdI|GACNNNN^NNGTC|GACCCCTCGGTC|970216|+
1   972180  .   G   A   403 PASS    ENZ=AgeI|A^CCGGT|ACCgGT|972177|+
1   1004957 .   G   A   316 PASS    ENZ=BsgI|GTGCAG(16/14)|gTGCAG|1004957|+
1   1004980 .   G   A   292 PASS    ENZ=BsePI|G^CGCGC|gCGCGC|1004980|+
1   1011087 .   CG  C   1052    PASS    ENZ=Eam1105I|GACNNN^NNGTC|GACTCTCAGTc|1011077|+
1   1017170 .   C   G   507 PASS    ENZ=AloI|(7/12)GAACNNNNNNTCC(12/7)|GAACAGAGcATCC|1017162|+