Topic
Chromosome naming
Why does bedtools return zero overlaps between my files?
UCSC uses chr1, Ensembl uses 1, and mitochondria are chrM, MT or chrMT depending on the source. Tools silently return nothing when names do not match, and the fix is a sed one-liner or a chromAlias table, not a re-run of the pipeline.
- How to Fix Chromosome Naming Mismatches in Variant Calling
Your BED file and your VCF look fine and bedtools says they share nothing: the cause is usually one prefix, and the repair is a text edit, not a re-run.