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

Sample intervals must be identical to the original intervals used to build the panel of normals



  • Official comment
    Samuel Lee

    When constructing the panel, you pass `-L intervals_list_hg19.bed` to CollectReadCounts.  However, for the case sample, you instead pass `-L targets_C.preprocessed.interval_list` to CollectReadCounts, which results in the mismatch error.

    It looks like you might want to pass `-L intervals_list_hg19.bed` to PreprocessIntervals, then pass the result via `-L` to CollectReadCounts for both the panel and the case samples.

    Comment actions Permalink
  • Avatar
    Pedro Miguel Raposo

    Thank you Samuel. That was indeed the problem!

    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk