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.

Mutect2 (v4.1.2.0) INDEL calling

Hi, wondering if there a limitation on indel calling with Mutect2. Although it called some validated INDELS (15bp del, 33bp ins, etc..), I have an 88bp deletion it did not. It was previously picked by HC (v3.2) at ~14% and with v4.1.2 as well at ~9.75%. I understand there will be differences between the two callers, but it is real and not present in PON to be filtered out. Just want to make sure if this is an expected outcome (due to indel length, any filters, etc..)

Re-posting here as seems to be the right place!

Answers

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