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!

Missing variants using the GATK best practices.


I am working with human whole exome (WES - Illumina, paired end) data and trying to perform variant calling by following the GATK best practices with GATK v4.1.2.0 installation(I know that there has been a new release few days back). GATK has been installed using conda config file as suggested on GATK installation page. Java version details are

openjdk version "1.8.0_192"
OpenJDK Runtime Environment (Zulu (build 1.8.0_192-b01)
OpenJDK 64-Bit Server VM (Zulu (build 25.192-b01, mixed mode)

I am comparing 2 variant datasets:

  1. DataSet#1
    Variant calling done using GATK best practices taking Illumina Exome Paired end data from NovaSeq S2: Nextera Flex for Enrichment (12-plex, NA12878) with Twist Human Core Exome (Illumina BaseSpace public data)

  2. DataSet#2
    VCF file downloaded from the same dataset from Illumina BaseSpace. Since the file (s55_NFE_Twist_NA12878-40M_S1.genome.vcf.gz) is genome VCF, it has been intersected with Twist exome BED file.

There are several SNV and INDELS which are present in DataSet#2 and not in DataSet#1 and we are trying to figure out why is that. For example, consider this region:

chr4:1388583 which has a SNV (A>G/G) for the gene CRIPAK present in DataSet#2 and not in DataSet#1.

What we have verified so far that:

--> This regions is well covered in DataSet#1 and DataSet#2.

--> That this region is present in the Twist Exome BED file that we are using

Could you provide us insights on how and what shall we do to compare the difference and figure out the exact reasons for the differences in the results. There are several such regions in both datasets.

Vijay Lakhujani


Sign In or Register to comment.