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 on October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.

size of gvcf generated by Haplotypecaller of 30x and 100x coverage of the same sample are different

I have a RAW reads with 30x and 100x coverage. When I followed all pre-processed steps as mentioned in GATK best practices to call variant. At last, gvcf files have been generated from both data by Haplotypecaller of GATK 4 but file size different. Why size of gvcf files are different, even same reference sequence was used in alignment by BWA mem? I think size of both gvcf files should be same if variants have been called by using same reference, same aligner i.e. BWA-mem with default parameters for both samples and same per-process steps were followed.
Sign In or Register to comment.