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

VariantRecalibrator Follow

3 comments

  • Avatar
    Marsha Wallace

    23-Sep-21 'Tutorial' link is broken

    0
    Comment actions Permalink
  • Avatar
    Zefeng Du

    Dear GATK team,

        It seems that the script provided for VariantRecalibrator has something wrong with the "--resource" augment.

        For example, using

    --resource hapmap,known=false,training=true,truth=true,prior=15.0:hapmap_3.3.hg38.sites.vcf.gz \

        will cause an user error indicating that the file doesn't exist. Instead, it works when I use

    --resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg38.sites.vcf.gz \

        I think it would be helpful if you fix the tutorial ASAP.

    1
    Comment actions Permalink
  • Avatar
    Rea Kalampaliki

    Hello! 

    Seems like the method documentation, parameters reccomendations and tutorial links link to the main page.

    0
    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk