variant calling with ALT contigs in hg38
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2.7 years ago
blueskypie ▴ 50

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!

next-gen • 1.7k views
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2.7 years ago
JC 12k

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.

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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.

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