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broadinstitute / gatk-protected

Obsolete/Legacy GATK repository -- go to https://github.com/broadinstitute/gatk instead
BSD 3-Clause "New" or "Revised" License
33 stars 20 forks source link

CNV PadTargets: tag doc and give example command #1093

Closed sooheelee closed 7 years ago

sooheelee commented 7 years ago

Pending questions

What exactly does the tool do to "behaves intelligently when padding consecutive targets naively would yield overlapping targets"? I think it's important to mention how the tool resolves overlaps in padding.

sooheelee commented 7 years ago

I now have the answer this my question -- it divides the overlapping region in half and gives each half to the upstream and downstream targets.

sooheelee commented 7 years ago

This is ready for review.

LeeTL1220 commented 7 years ago

@sooheelee So long as the tests pass, squash and merge away.