Topic
Genome build mismatches
Are all my files on the same reference build?
hg19 and hg38 coordinates differ by kilobases to megabases, and a BED file from one build against a BAM from the other produces confident, wrong overlaps. The check is cheap: contig lengths in the header and a few known landmark genes.
- How to Catch a Genome Build Mismatch in Variant Calling
A BED file from the wrong build gives you confident, wrong overlaps, and the header check that catches it takes thirty seconds.