Test-drive the GATK tools and Best Practices pipelines on Terra


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question in recapseg .pcov file

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

Inputs
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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 .pcov.cr.stat 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.

Outputs
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  • panel of normals file (hdf5)
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