VcfFilterGtf

Filter VCF on GTF

Usage

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

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

Usage: vcffiltergtf [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
    --biotype
      What biotype 'x'  should be used.
      Default: all
      Possible Values: [all, protein_coding]
    --extend, --extends, -x
      extends each gtf feature by 'x' bases.A distance specified as a positive 
      integer.Commas are removed. The following suffixes are interpreted : 
      b,bp,k,kb,m,mb,g,gb 
      Default: 0
    --gene_id
      Optional file containing a list of gene IDs . Filter on attribute 
      gene_id 
    --gene_name
      Optional file containing a list of gene names . Filter on attribute 
      gene_name 
    --generate-vcf-md5
      Generate MD5 checksum for VCF output.
      Default: false
  * -gtf, --gtf
      GTF file
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --inverse
      inverse output
      Default: false
    -o, --out
      Output file. Optional . Default: stdout
  * -t, --type
      What should be used in the gtf to keep vcf records
      Default: GENE
      Possible Values: [GENE, TRANSCRIPT, EXON, EXON_BOUDARIES]
    --version
      print version and exit

Keywords

• vcf
• gtf

Creation Date

20230703

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfgtf/VcfFilterGtf.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 vcffiltergtf ? 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

Motivation

filter a VCF with a GTF. I'm fed up to filter a GTF, convert the GTF to bed and use the bed to filter the GTF.