jvarkit

BimToVcf

convert a .bim to a .vcf . For @FlorianeS44

Usage

Usage: bim2vcf [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, --output
      Output file. Optional . Default: stdout
  * -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard CreateSequenceDictionary
    --version
      print version and exit

Keywords

• bim
• vcf

Compilation

Requirements / Dependencies

• java compiler SDK 11. Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew bim2vcf

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

Source code

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

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/misc/BimToVcfTest.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 bim2vcf ? 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

Contig conversion

chromosome 23 is converted to X or chrX, chromosome 24 is converted to Y or chrY, chromosome 25 is ignored, chromosome 26 is converted to chrM or MT.

Example

$ java -jar dist/bim2vcf.jar -R human_g1k_v37.fasta input.bim 

##fileformat=VCFv4.2
##INFO=<ID=MORGAN,Number=1,Type=Float,Description="Centimorgan">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Variation type">
##contig=<ID=1,length=249250621,assembly=human_g1k_v37>
(...)
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
1       12      rs73422 C       .       .       .       MORGAN=0.5224;SVTYPE=NOVARIATION
1       13      rs30315 G       A       .       .       MORGAN=0.530874;SVTYPE=SNV
1       14      rs14325 C       T       .       .       MORGAN=0.532596;SVTYPE=SNV
1       15      rs31319 A       G       .       .       MORGAN=0.532682;SVTYPE=SNV
1       16      rs954   C       T       .       .       MORGAN=0.537655;SVTYPE=SNV
1       17      rs62034 G       A       .       .       MORGAN=0.548645;SVTYPE=SNV
1       18      rs25996 A       G       .       .       MORGAN=0.575595;SVTYPE=SNV
1       19      rs12117 G       A       .       .       MORGAN=0.582608;SVTYPE=SNV
(...)

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