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

ASEReadCounter java.lang.ArrayIndexOutOfBoundsException: 0

0

3 comments

  • Avatar
    Bhanu Gandham

    zhaol

    Seems to me that there is still an issue with the new bam file. Can you please try these suggestion:

    1. You mentioned you fixed the bam, how did you do that?
    2. Please run validateSamFile on the corrected bam and ValidateVariants on the vcf again to confirm their validity. 
    3. Please check if the bam file and the vcf were generated using the same reference
    4. One other thing to try if none of the other above mentioned suggestions work is to re-run ASEReadCounter with a reference as input.

     

     

     

    0
    Comment actions Permalink
  • Avatar
    zhaol

    Hi, Bhanu Gandham.

    First, I fixed BAM with the FixmateInformation program.After I fix BAM, I re-run the ValidatArray and ValidatesSamFile and no error messages are displayed.

    Second, I need to reconfirm with my colleagues that the reference used is the same.

    Finally, I add the -R parameter and the reference and find that the program runs.

    0
    Comment actions Permalink
  • Avatar
    Bhanu Gandham

    That's good! Good to know that using the reference solves the problem. It is possible that the tool requires some information not available in the bam file and hence providing a reference solves the issue. 

    0
    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk