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.
PF reads / Illumina chastity filter
Illumina sequencers perform an internal quality filtering procedure called chastity filter, and reads that pass this filter are called PF for pass-filter. According to Illumina, chastity is defined as the ratio of the brightest base intensity divided by the sum of the brightest and second brightest base intensities. Clusters of reads pass the filter if no more than 1 base call has a chastity value below 0.6 in the first 25 cycles. This filtration process removes the least reliable clusters from the image analysis results.
For additional information on chastity filters, please see:
- Illumina, Inc. (2015). Calculating Percent Passing Filter for Patterned and Non-Patterned Flow Cells: A comparison of methods for calculating percent passing filter on Illumina flow cells
- Ilumina Inc. (2014) HiSeq X System user guide
Both articles can be found at http://www.Illumina.com