Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!

Does GATK variant discovery make use of unpaired alignments and discordant alignments?

I've searched for this and cannot find the answer. Suppose a BAM file contains Illumina paired-end reads with the following types of alignments:

1) Properly paired alignments (both mates mapped with the proper orientation and within the expected distance)
2) Discordant pairs (both mates are mapped, but not properly paired)
3) Unpaired alignments (singletons, only one of the mates is mapped)

Does the GATK variant discovery process make use of the discordant pairs and unpaired alignments? If so, what would be the consequence of excluding the discordant pairs and singletons?


  • SheilaSheila Broad InstituteMember, Broadie admin


    I think HaplotypeCaller uses all properly mapped reads in analysis. Perhaps this thread will help too.

    In good quality "clean" regions, the assumption is that there won't be many discordant pairs or unpaired alignments, so discounting those should not make much difference.


Sign In or Register to comment.