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sjanssen2 / spike

NGS pipeline for SNV detection in tumor context
BSD 3-Clause "New" or "Revised" License
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new capture kit V7 #219

Open deyazoubi opened 5 years ago

deyazoubi commented 5 years ago

there are three ways to define the capture kit for a sample:

  1. by adding a column "capture_kit" to the input samplesheet and set the cell value to a capture kit name defined in config.yaml see 180222_K00171_0649_HT332BBXX_spike.csv
  2. by specifing a key "capture_kit" at the project in config.yaml. Value must match one of the defined capture kits in config.yaml

  3. by specifing the species for the project, which than select the default kit defined in config.yaml for the species.

    1,2,3 are listed in order of their precedence, i.e. of 1 and 3 is defined, 1 wins.

https://github.com/sjanssen2/spike/blob/ee9f8f9f0e7147ec46cc83f8f022f5097b492e28/config.yaml#L199

deyazoubi commented 4 years ago

config.yaml capture_kit: we are using two default capture kits for human and for mouse. This might change in the future and thus you can define a project specific capture_kit.

Assay: the capture kit, like Agilent_Sure_SelectXT