jvarkit

VcfPhased01

X10 Phased SVG to Scalar Vector Graphics (SVG)

Usage

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

Usage: java -jar dist/jvarkit.jar vcfphased01  [options] Files

Usage: vcfphased01 [options] Files
  Options:
    -xp, --xpos, --extra-highligth
      Extra Highligth positions that are not always in the vcfs. (existing 
      file with one position per line or string 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. (existing file with one position per 
      line or string comma separated)
      Default: <empty string>
  * -r, --interval, --region
      interval CHROM:START-END
    -k, --knownGenes
      Transcrips as genpred format 
      https://genome.ucsc.edu/FAQ/FAQformat.html#format9  . The genePred 
      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)
    -o, --output
      Output file. Optional . Default: stdout
    --version
      print version and exit

Keywords

• x10
• phased
• genotypes
• svg

See also in Biostars

• https://www.biostars.org/p/9462569

Creation Date

20190710

Source code

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

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