Can I skip the step that incorporate the coverage biases in HSats?

[ericgonzalezs]

Hi,

I would like to run this pipeline in a plant genome. I would like to skip the step4 "incorporation coverage biases in HSats". How I could achieve this if I want to run "flagger_end_to_end_no_variant_calling_no_ref.wdl"?.

Many thanks.

[mobinasri]

Hi @ericgonzalezs

Yes you can use "flagger_end_to_end_no_variant_calling_no_ref.wdl" using the instructions mentioned here:
https://github.com/mobinasri/flagger#running-pipeline-with-wdl
It ignores incorporation coverage biases in HSats.