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Member
edited March 2013

Hi
Is it possible to set the maximum insert size allowed for the MaxInsertSize read filter? Looking at the documentation at http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_filters_MaxInsertSizeFilter.html it's set with a default value of 1,000,000 which is too high for what we want.

If it is possible how does one set it I've tried several different combinations and nothing seems to work, apart from leaving it with it's default value. Reading the doc it looks like --maxInsertSize 1000 should work, but GATK refuses to accept that complaining the 1000 is an unknown argument.

I've tried -rf MaxInsertSize GATK runs with that as long as I don't try to supply a number to adjust the default value.
So -rf MaxInsertSize 1000, -rf MaxInsertSize=1000,-maxInsertSize=1000,-maxInsertSize 1000 etc don't work though looking at the docs I would have thought at least one of them would have.

Thanks

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• Member

Thank you that solves the issue. I'd not have guessed that the answer was -rf MaxInsertSize -maxInsertSize 1000!
Is this clearly stated in the Docs? If not may be worth adding!

Thanks!

Well, it's in the docs here: http://www.broadinstitute.org/gatk/guide/article?id=1323

But admittedly it's at the end of a page targeted at developers. I'll put this in a FAQ article to make it more obvious.

• Member

How does this filter work? Does it look at the coordinates for the mapped read pair?