If you happen to see a question you know the answer to, please do chime in and help your fellow community members. 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.
TruSeq Libraries influence in PON
We are trying to build a PON to use with MuTect2 GATK4. Our samples are sequenced using the library TruSeq Nano DNA 350. How important would be that the samples of the PON have exactly the same library? Would be fine if they were sequenced with TruSeq DNA PCR-free or with TruSeq DNA? We are trying to build it using samples from SRA, and there is just one sample from a healthy individual using our configuration (Illumina HiSeq 2x150 TruSeq NanoDNA350).
Thank you very much,
Tamara and Laura