I came across a slide share about the new GRCh38 assembly and its ALT_LOCI assemblies. (http://www.slideshare.net/vaschn/agbt2014schneider)
Question: 1. Are there any "ALT Loci aware" aligners out there ?
- If so, then how are accommodating these ALT LOCI while aligning reads to the reference genome ? How do they chose between primary assembly and Alternate Loci ?
Some references: This Biostar thread (Applying patches to GRCh assembly) talks about patches/Alts during alignment as well as about the aligner - srprism (ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/srprism)
Nice overview of ALT LOCI in GRCh38 (Will GRC38/HG20 be a multiple sequence reference genome?)
thanks in Advance,