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

SplitNCigarReads: Contig ERCC-ERCC-00002 given as location, but this contig isn't present in the Fasta sequence dictionary



  • Avatar
    Gökalp Çelik

    Hi Cora Olpe

    This problem is about reference vs bam incompatibility and unless your alignment files are 1:1 match with your reference fasta file our tools will not work properly and throw these errors. Unfortunately the only sane way to resolve this issue is to realign your reads to the reference you have or try to obtain the original reference that was used by the sequencing center that you received your bam files. 

    I hope this helps. 

    Comment actions Permalink
  • Avatar
    Cora Olpe

    Hi Gökal Celik, 

    alright, that sounds like I can solve it, I've contacted the people for the original reference. Thank you!

    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk