Is there any filtering required on Gemini output?

[BrettLiddell]

Hello,

I ran Gemini on some bam files and 17% are PerfectStitched. I did variant calling and when looking in IGV I saw that some reads were annotated FailStitch. However, if I understand correctly, this is just the result of a first try at stitching and Gemini either attempts stitching again or uses the original reads? I thought I should clarify rather than make an assumption though: are there any annotations for stitched reads that indicate they should be filtered out, or am I okay to keep everything? I appreciate any advice!

[tamsen]

Hi Brett,

No additional filtering is needed. Yes, if reads fail stitching they will still be retained and used.

best
Tamsen

[BrettLiddell]

Thank you!