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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!
Multi-sample calling vs single sample calling
Dear GATK team,
I have used the UG following the best practice GATK workflow to call snps and Indels from exomeseq data of 24 human samples. First I called snps and Indels separately for each bam file, and I obtained separate vcfs. Then I decided to try to call the snps and Indels all in one go. I noticed that the output was quite different and the number of inser/delitions was higher when I called variants in contemporary (starting from separate bam files: -I sample1.bam -I sample2.bam...ETC). I also noticed that the called indels mostly were adjacent to tricky areas such as repetitive elements (ATATATATATATAT) or next to polyAAAAA. These snps and Indels weren't called by the UG when I called the variants separately. Is it more error prone to call variants in contemporary?