Counting total variants

Question

[Hadi M]

Hello,

I am curious of how normally variant researchers count their variants. The full assembly of GRCh38 contains the primary assembly (chromosome 1:22, X and Y), mitochondrial genome, some patches and alternate locus. After variant calling, do they only count the variants from the entire assembly (including the alternate locus) or do they just count the variants that fall within the primary assembly plus the mitochondrial genome?

Cheers :)

Answer 1

[finswimmer]

Hello,

of course this depends of the goal of your study. Most people will not include patches and alternate loci to the reference they align to. See the explanation in this tutorial I wrote some time ago.

fin swimmer

[ATpoint]

As finswimmer said, you should decide that based on the question you want to answer. Lets say you only sequenced women as part of a ovarian cancer study and still had chrY in the reference fasta, I would for example omit variants on that one. Total mutation count is also not too informative as the majority simply represents personal variation from the reference genome without rendering any phenotype.

[Hadi M]

Thank you very much both of you and thanks for the feedback at the end ATpoint, will keep that in mind :). Cheers