Count reads fully spanning tandem repeats

nspies / svviz2

for visual evaluation of read support for structural variation

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Count reads fully spanning tandem repeats #28

Open jzook opened 7 years ago

jzook commented 7 years ago

In tandem repeats, it's often important to know whether reads fully span a tandem repeat in order to know whether the ALT or REF call is actually correct. I'd expect it would be useful to have an annotation related to the count of reads that support ALT and REF and fully span any repeats at the breakpoints plus ~20 bp on either side.

nspies commented 7 years ago

To clarify that I understand correctly, we should:

find repeats that overlap any breakpoint
for each such repeat, count how many reads fully span that repeat plus x bp to either side

Then it should be possible to see from the report:

which breakpoints have overlapping repeats
of those breakpoints that are repetitive, how many reads fully span those repeats