I want to know sequence_group_intervals in fivedollar-genome-anlalysis pipeline

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BI_joy

• March 11, 2020 08:53
• Edited

a) GATK version used

gatk 4.1

b) Exact GATK commands used

i want to know option -L in BaseRecalibrator

Hi 

In fivedollar-genome-analysis pipeline. I ran BaseRecalibrator

then I have a question

-L option is file that made by gatk SplitIntervals or use wgs_calling_regions.hg38.interval_list in gatk resource bundle?? 

If made by gatk SplitIntervals, how can i set a number of --scatter-count option??

 

Thank you for listening to my concerns.

 

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  Bhanu Gandham

  • March 19, 2020 00:00

  Responded to user via email. 

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