You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
The genome is complex, not because of the ALT contigs. The ALT contigs will still be the way of next GRCh39?
For SNP/small INDEL, most of job will be done by ALT-aware align such as bwa.kit or novoalign.
For SV, we will need a genome struct (alt-contig, fix-patchs) aware caller.
As I reflect now, I think the logic behind ALT contigs is flawed or is a temporary hack at best. You don't need ALT contigs for most analyses and so far no one understands how to properly use ALT contigs. Also, there won't be GRCh39 as I understand.
Hi.
There is no needs of alt-aware for long reads because there is enough info to map it to primary or alt sequence in GRCh38 reference genome.
but we need it for short reads(-x sr) such as run-bwamem/bwa.kit?
Best Regards
The text was updated successfully, but these errors were encountered: