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Grch38 And Reference Alignment

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 ?

  1. 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,

Aniket

human alignment
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updated by deanna.church deanna.church • written by aniketd86 aniketd86

1 answer

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

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.

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written by deanna.church deanna.church

Deanna, thanks for the prompt answer ! Do you know of any variant callers making use of the multi-allelic reference.( future versions of GATK maybe) ? Also, how do you think variants on primary and alt sequences would be represented in a VCF file [Flag in the INFO col or list the same variant twice ] ?

• 216 views • link
written by aniketd86 aniketd86

I know of no variant callers that have been modified to handle this. sorry. :(

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written by deanna.church deanna.church

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