GatkHaplotypeCaller

Wrapper for GATK HaplotypeCaller

Usage

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

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

Usage: gatkhc [options] Files
  Options:
  * -L, -bed, --bed
      restrict to bed
    -dbsnp, --dbsnp
      path to dbsnp
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --mapq
      mapping quality
      Default: 10
    -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
    --references
      Other references. If a reference is different from the main reference, 
      the contigs of a  GVCF file will be converted (e.g: 1 -> chr1) to the 
      main reference dictionary.
      Default: []
    --tmp, --tmp-dir
      temporary directory
      Default: /tmp
    --version
      print version and exit

Keywords

• gatk
• vcf
• bam

Creation Date

20240625

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/gatk/GatkHaplotypeCaller.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 gatkhc ? 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

This tool is a wrapper over gatk4 HaplotypeCaller

Not All versions of jvarkit will work for this tool. Because it needs to be compiled against the java code from gatk using a command like:

./gradlew jvarkit -Dgatk4.local.jar=/path/to/gatk/gatk-package-4.*-local.jar

Furthermore, don't trust the automatic generated documentation, the tool must be invoked using the following syntax:

java -cp /path/to/jvarkit.jar:/path/to/gatk-package-4.xxx-local.jar \
    com.github.lindenb.jvarkit.tools.gatk.GatkHaplotypeCaller \
    -R src/test/resources/rotavirus_rf.fa \
    --bed input.bed \
    src/test/resources/S*.bam

This tool:

• call each BAM into a .vcf.gz using haplotype caller
• convert the dictionary/chromosomes if needed
• convert the sample name if the same sample if present more than once
• group g.vcf.gz files by the sqrt(number-of-gvcf-files)
• combine each group of gvcf files
• genotypegvcfs for the final gvcf file