jvarkit

VcfTail

Last commit

print the last variants of a vcf

Usage

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

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

Usage: vcftail [options] Files
  Options:
    -c, --bycontig
      Print first variant for each contig; Implies VCF is sorted
      Default: false
    --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
    -n, -N, --count
      number of variants
      Default: 10
    --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
    --version
      print version and exit

Keywords

Creation Date

20131210

Source code

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

Unit Tests

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

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite vcftail ? 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

$  curl -s "https://raw.github.com/arq5x/gemini/master/test/test1.snpeff.vcf" |\
java -jar dist/vcftail.jar -n2 |\
grep -v "##"| cut -f 1,2,4,5

#CHROM  POS REF ALT
chr1    935492  G   T
chr1    1334052 CTAGAG  C
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