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.

Spurious insertions being called by HaplotypeCaller?

David_RDavid_R United StatesMember

I just called variants from the same bwa-generated bam file using 1) samtools/bcftools and 2) HaplotypeCaller.

Downstream analysis indicated that a particular locus looked interesting, but only in the GATK output. When I looked up the position in the vcf files, the samtools vcf file showed no variant at this position while the GATK vcf file showed a single nucleotide insertion.

Viewing the bam file in IGV shows no insertion at this site and very good read depth (>100x) and mapping quality. There is an insertion 10nt away

Is there anything known that might cause such behavior? Are there any parameters in HaplotypeCaller that might make insertion assignments more likely?

Thank you

Best Answer


  • David_RDavid_R United StatesMember

    Yes, there are reads in the region with softclipped ends, so I guess using the option "--dontUseSoftClippedBases" would be the test here. And I think I understand why softclipped reads are considered by HaplotypeCaller by default. If I look turn on soft clipped bases in IGV, I can see the same insertion in both our "case" pooled sample and "control" pooled sample. This seems like a good illustration of why I should try using joint haplotype calling, yes?

  • SkyWarriorSkyWarrior TurkeyMember ✭✭✭
Sign In or Register to comment.