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

MerVcfs did not work


1 comment

  • Avatar
    Pamela Bretscher

    Hi chenglei,

    MergeVcfs requires that all of your input vcf files have the exact same samples which you can read about in the tool documentation. Therefore, there most likely isn't anything wrong with the vcf files you created, but the "SCA_917_N.germline_raw.vcf" has samples in it that are not present in your other file. 

    Kind regards,


    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk