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

How can I get Sample Summary


1 comment

  • Avatar
    Pamela Bretscher

    Hi rq m,

    Thank you for writing in. I'm not sure I understand what metrics you are wanting that are not present in your VariantEval output. It looks like the number of SNPs and MNPs per sample is being shown under "CountVariants" as "nSNPs" and "nMNPs" and indel numbers are calculated by "IndelSummary" as "n_indels" in your output. Please let me know if this is not the output and metrics you are looking for. 

    Kind regards,


    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk