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if panel and wes data not using corresponding bed, except for time, is there other errors?

hi, thanks a lot.
in https
you give detailed talk about when need bed file.

here I want to confirm with you two things.

if using targeted panel and wes, I do not use bed, except for time and computer consumption, is there any other wrong?(both germline and somatic)

the step BQSR and applybqsr , should I use bed file

thanks a lot
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