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

MergeBamAlignment (Picard) Follow

1 comment

  • Avatar

    When I use gatk MergeBamAlignment to merge an unmapped bam and a mapped file, it always generates following information:
    PicardException: Second read from pair not found in unmapped bam: DP8400021549TLL1C001R00501671426, DP8400021549TLL1C001R00501688673
    I tried to use FixMateInformation to fix it and found:
    SAMException: Found two records that are paired, not supplementary, and first of the pair

    Such errors are common. I would be grateful if you could help me understand what I can do to resolve these errors.


    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk