How does variant callers deal with N in the reference sequence?

Question

[pyjiang2]

If there is an N in the reference genome, after the variant calling pipeline, if an alternative base (A/T/G/C) is called at the same position, will it be output in the VCF? Or any variants with the N in the reference will be ignored? Thanks!

Answer 1

[JC]

In general, such positions are ignored.