IbdToVcf

IBD data to VCF

Usage

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

Usage: java -jar dist/jvarkit.jar ibd2vcf  [options] Files

Usage: ibd2vcf [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
  * -B, --bed, --markers
      Marker file chrom(tab)start(tab)end(tab)name
    --maxRecordsInRam
      When writing  files that need to be sorted, this will specify the number 
      of records stored in RAM before spilling to disk. Increasing this number 
      reduces the number of file  handles needed to sort a file, and increases 
      the amount of RAM needed
      Default: 50000
    -o, --output
      Output file. Optional . Default: stdout
  * -P, --fam, --pedigree
      Pedigree file. family-id(space)sample-id.
  * -R, --reference, --dict
      A SAM Sequence dictionary source: it can be a *.dict file, a fasta file 
      indexed with 'picard CreateSequenceDictionary' or 'samtools dict', or 
      any hts file containing a dictionary (VCF, BAM, CRAM, intervals...)
    --tmpDir
      tmp working directory. Default: java.io.tmpDir
      Default: []
    --version
      print version and exit

Keywords

• ibd
• vcf

Creation Date

20210701

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/ibddb/IbdToVcf.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 ibd2vcf ? 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

` $ java -jar dist/ibd2vcf.jar --fam TSF.fam --bed TSF.bed -R human_b37.dict TSF_Chr22.ibdtxt |\ bcftool view -O b -o out.bcf