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.

question in recapseg .pcov file

I had a question in recapseg. I would like to ask more clarification how to generate .pcov and file.

All file lists must have corresponding entries. These files will correspond to control/normal samples.

  • control_pcov_file_list -- text file listing file paths to .pcov files. One entry per line.
  • control_cr_stat_file_list -- text file listing file paths to files. One entry per line.
  • control_sample_id_list -- list of sample ids for the corresponding pcov and cr stat files. One entry per line.


  • panel of normals file (hdf5)


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