Question: Why do I see variants outside of the target region with the
longranger targeted pipeline?
Answer: Long Ranger intentionally ignores the target_file BED when calling variants. We let the variant caller find variants anywhere there is coverage. It's very common to have coverage on a variant just outside the target region, and find a SNP there. We can then use these SNPs to do better phasing. This makes the phasing results on exome significantly better.
For more information on
longranger targeted please see Targeted Phasing and SV Calling.