Minimap2: primary/alt-aware for short reads(-x sr)?

[wangyugui]

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

[lh3]

Minimap2 doesn't and won't work with ALT contigs. So far ALT contigs complicate everything but deliver little benefit.

[wangyugui]

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.

[lh3]

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.