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Default read filters applied by GATK

adamhadamh Cambridge, MAMember

Hi,
Where can I find a list of the default read filters that are applied by GATK tools, specifically by the ClipReads tool.
The documentation says that:

These Read Filters are automatically applied to the data by the Engine before processing by ClipReads.
MalformedReadFilter
BadCigarFilter

Is that all of the filters that are applied?
Thanks!

Answers

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