Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

GATK process banner

Need Help?

Search our documentation

Community Forum

Hi, How can we help?

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

HaplotypeCaller Follow

1 comment

  • Avatar
    David Parry

    The "Single-sample GVCF calling with allele-specific annotations" example is out of date. The example annotation groups no longer work in this version of GATK.

    The example should read:

    gatk --java-options "-Xmx4g" HaplotypeCaller  \
       -R Homo_sapiens_assembly38.fasta \
       -I input.bam \
       -O output.g.vcf.gz \
       -ERC GVCF \
       -G StandardAnnotation \
       -G AS_StandardAnnotation
    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk