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# disable NotPrimaryAlignmentFilter in DepthOfCoverage

Member Posts: 1

Can someone point me to documentation on how I can run DepthOfCoverage without the NotPrimaryAlignmentFilter?

Tagged:

It's not possible to disable filters that are on by default, sorry.

Geraldine Van der Auwera, PhD

• Member Posts: 3

"It is intended to ensure that only reads that are likely to be mapped in the right place, and therefore to be informative[...]"

I disagree:
This filter removes reads sequenced from the repeat regions, where reads shall map as many times as there are repeated region.
This is their rightful place. This filter won't allow us to deal with repeat regions (with the depth of coverage).
May be it can be very useful, in that case, to add a small function to allow us to disable default filter.

Regards,

Rémi