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

Badly formed genome unclippedLoc: Contig chr1_KI270766v1_alt given as location, but this contig isn't present in the Fasta sequence dictionary



  • Avatar
    Aaron Seo


    I think I figured out the issue:

    There were "*_alt" chromosomal designations in my interval list (.bed file)--- I removed these, and mutect2 ran successfully. 


    Thank you!

    Comment actions Permalink
  • Avatar
    Gökalp Çelik

    Hi Aaron Seo

    We are glad that you solved the issue. Thank you for sharing it. 


    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk