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?
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.
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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