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

mobinasri / flagger

Evaluating genome assemblies

MIT License

58 stars 4 forks source link

Can I skip the step that incorporate the coverage biases in HSats? #23

Open ericgonzalezs opened 1 year ago

ericgonzalezs commented 1 year ago

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 commented 1 year ago

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.