Question

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

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6.5 years ago

pyjiang2 ▴ 40

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!

reference-genome variant-calling • 1.1k views

ADD COMMENT • link updated 23 months ago by Ram 44k • written 6.5 years ago by pyjiang2 ▴ 40

score 2 · Accepted Answer · 2018-06-11

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6.5 years ago

JC 13k

In general, such positions are ignored.

ADD COMMENT • link 6.5 years ago by JC 13k