variant calling with ALT contigs in hg38

Question

[blueskypie]

After reading the Board Institute tutorial on variant calling with ALT contigs, just wonder if anyone can advise the scenario it is preferred over calling w/o ALT contigs? and any public study using variant calling with ALT contigs?

Thanks!

Answer 1

[JC]

The basic scenario is when you expect your individual not so close to the reference genome, the use of the ALT contigs can provide a better alignment then.

[ATpoint]

One should add here that the ALT contigs are only about 109Mb in total from which are about 60Mn on the primary assembly, so less than 2% of the entire genome. You should first make sure that the ALTs actually comprise regions that are interesting for your research goal, such as HLA loci. If not, I do not see the benefit.