BedToVcf

Convert BED file to VCF, finding REF allele at start and 'N' as ALT allele

Usage

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

Usage: java -jar dist/jvarkit.jar bed2vcf  [options] Files

Usage: bed2vcf [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
    --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
  * -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict
    -s, --symbolic
      use symbolic REF allele if bed length > 'x'. 'x' <=0 to disable
      Default: 100
    --version
      print version and exit

Keywords

• bed
• vcf

Creation Date

20240604

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/bed2vcf/BedToVcf.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 bed2vcf ? 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

Convert BED file to VCF, finding REF allele at start and 'N' as ALT allele. The VCF can be used later for genotyping.

input is a set of BED file or one file with a '.list' extension containing the path to the BED files.

Example

$ bcftools query -f '%CHROM\t%POS0\t%END\n' src/test/resources/rotavirus_rf.vcf.gz |\
    java -jar dist/jvarkit.jar bed2vcf -R src/test/resources/rotavirus_rf.fa | head -n 30

##fileformat=VCFv4.2
##contig=<ID=RF01,length=3302>
##contig=<ID=RF02,length=2687>
##contig=<ID=RF03,length=2592>
##contig=<ID=RF04,length=2362>
##contig=<ID=RF05,length=1579>
##contig=<ID=RF06,length=1356>
##contig=<ID=RF07,length=1074>
##contig=<ID=RF08,length=1059>
##contig=<ID=RF09,length=1062>
##contig=<ID=RF10,length=751>
##contig=<ID=RF11,length=666>
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO
RF01    970 .   A   N   .   .   .
RF02    251 .   A   N   .   .   .
RF02    578 .   G   N   .   .   .
RF02    877 .   T   N   .   .   .
RF02    1726    .   T   N   .   .   .
RF02    1962    .   TACA    N   .   .   .
RF03    1221    .   C   N   .   .   .
RF03    1242    .   C   N   .   .   .
RF03    1688    .   T   N   .   .   .
RF03    1708    .   G   N   .   .   .
RF03    2150    .   T   N   .   .   .
RF03    2201    .   G   N   .   .   .
RF03    2315    .   G   N   .   .   .
RF03    2573    .   A   N   .   .   .
RF04    887 .   A   N   .   .   .
RF04    991 .   T   N   .   .   .
RF04    1241    .   T   N   .   .   .