<p>I came across a slide share about the new GRCh38 assembly and its ALT_LOCI assemblies.
(<a href='http://www.slideshare.net/vaschn/agbt2014schneider'>http://www.slideshare.net/vaschn/agbt2014schneider</a>)</p>

<p>Question: 
1. Are there any "ALT Loci aware" aligners out there ?</p>

<ol>
<li>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 ?</li>
</ol>

<p>Some references: 
This Biostar thread (<a href='/p/45788/'>Applying patches to GRCh assembly</a>) talks about patches/Alts during alignment as well as about the aligner - srprism (<a href='ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/srprism'>ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/srprism</a>)</p>

<p>Nice overview of ALT LOCI in GRCh38 (<a href='/p/59126/'>Will GRC38/HG20 be a multiple sequence reference genome?</a>)</p>

<p>thanks in Advance,</p>

<p>Aniket </p>

<p>There are two 'ALT loci aware' (or multi-allelic reference) aware aligners that I know about. </p>

<ul>
<li>srprism (<a href='ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/srprism'>ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/srprism</a>)</li>
<li>ibwa (<a href='https://github.com/genome/ibwa'>https://github.com/genome/ibwa</a>)</li>
</ul>

<p>Neither are published (AFAIK) but srprism is in preparation. In general, I think they both need to be tested more. 
It is also unclear how other tools along the tool chain (variant calling) will respond- and they will likely also need modification to take advantage of the full assembly.</p>
