jvarkit

VcfPhased01

Last commit

X10 Phased SVG to Scalar Vector Graphics (SVG)

Usage

Usage: vcfphased01 [options] Files
  Options:
    -xp, --xpos, --extra-highligth
      Extra Highligth positions that are not always in the vcfs. (comma 
      separated) 
      Default: <empty string>
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -p, --pos, --highligth
      Highligth positions in the VCFs. (comma separated)
      Default: <empty string>
  * -r, --interval, --region
      interval CHROM:START-END
    -k, --knownGenes
      UCSC knownGene File/URL. The knowGene format is a compact alternative to 
      GFF/GTF because one transcript is described using only one line.	Beware 
      chromosome names are formatted the same as your REFERENCE. A typical 
      KnownGene file is 
      http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz 
      .If you only have a gff file, you can try to generate a knownGene file 
      with [http://lindenb.github.io/jvarkit/Gff2KnownGene.html](http://lindenb.github.io/jvarkit/Gff2KnownGene.html)
      Default: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/wgEncodeGencodeBasicV19.txt.gz
    -o, --output
      Output file. Optional . Default: stdout
    --version
      print version and exit

Keywords

See also in Biostars

Compilation

Requirements / Dependencies

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew vcfphased01

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

Creation Date

20190710

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/phased/VcfPhased01.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite vcfphased01 ? 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

For @154sns , 10 July 2019

Displays phased genotypes from X10 genomics into SVG.

Input

input is a list of indexed vcf files or a file with the suffix ‘.list’ containing the full path to the vcfs

Example

find . -type f -name "*.vcf.gz" > in.list
java -jar dist/vcfphased01.jar -r "chr1:1000-2000" -xp '1001,1010' in.list 

Screenshots

https://twitter.com/yokofakun/status/1148964221482414080

https://pbs.twimg.com/media/D_Hwd2dXoAAzx8g.jpg