jvarkit

StructuralVariantToFasta

convert VCF of structural variant(s) to fasta for pggb

Usage

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

Usage: java -jar dist/jvarkit.jar sv2fasta  [options] Files

Usage: sv2fasta [options] Files
  Options:
    --exclude-filtered
      Exclude FILTER-ed variants.
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
  * -r, --region, --interval
      interval. An interval as the following syntax : "chrom:start-end" or 
      "chrom:middle+extend"  or "chrom:start-end+extend" or 
      "chrom:start-end+extend-percent%".A program might use a Reference 
      sequence to fix the chromosome name (e.g: 1->chr1)
    -o, --output
      Output file. Optional . Default: stdout
  * -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict
    --skip-no-sv
      Exclude VCF without structural variant
      Default: false
    --version
      print version and exit

Keywords

• vcf
• cnv
• fasta

Creation Date

20230403

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/sv2fasta/StructuralVariantToFasta.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 sv2fasta ? 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

create a fasta input for pggb (pangenome graph builder)

input

input is a set of indexed VCF files or a file with the suffix ‘.list’ containing the path to the VCFs

example

java -jar dist/jvarkit.jar sv2fasta --interval "chr1:204091-325320" --skip-no-sv --exclude-filtered -R ref.fasta vcfs.list > tmp.fa

samtools faidx tmp.fa

pggb -i tmp.fa \
	-o OUT \
    -n `grep ">" tmp.fa | wc -l` \
	-p 90 -s 100 \
	-t 5 1>&2

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