jvarkit

ConvertVcfChromosomes

Last commit

Convert the names of the chromosomes in a VCF file

DEPRECATED

use bcftools annotate with --rename-chrs file (does it handle BND ALT alleles ?)

Usage

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

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

Usage: vcfrenamechr [options] Files
  Options:
    --fatal
      exit with failure if a conversion fails. Default: skip the variant
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
  * -f, --mapping, -m
      Chromosome mapping file. If the file looks like a NGS file (fasta, vcf, 
      bam...) the mapping is extracted from a dictionary; Otherwise, it is 
      interpreted as a mapping file ( See 
      https://github.com/dpryan79/ChromosomeMappings )
    -o, --out
      Output file. Optional . Default: stdout
    --version
      print version and exit

Keywords

vcf
contig
chromosome
convert

Source code

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

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/misc/ConvertVcfChromosomesTest.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 vcfrenamechr ? 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

Deprecated

use bcftools annotate with --rename-chrs file

rename chromosomes according to the map in file, with “old_name new_name\n” pairs separated by whitespaces, each on a separate line.

Example

$ curl  "https://raw.github.com/arq5x/gemini/master/test/test5.vep.snpeff.vcf" |\
  java -jar dist/vcfrenamechr.jar -i -C -f src/main/resources/chromnames/hg19_to_g1kv37.tsv |\
cut -f 1-5

(...)
##contig=<ID=1,length=249250621>
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##reference=file:///m/cphg-quinlan/cphg-quinlan/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa
#CHROM	POS	ID	REF	ALT
1	145273345	.	T	C
1	156011444	.	T	C
5	64982321	.	T	C
10	1142208	.	T	C
10	126678092	.	G	A
10	135210791	.	T	C
13	48873835	.	G	A
20	36779424	.	G	A
X	17819377	.	T	C