Question: Grch38 And Reference Alignment
11
gravatar for aniketd86
17 months ago by
aniketd86110
Cambridge, MA
aniketd86110 wrote:

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

ADD COMMENTlink modified 17 months ago by deanna.church930 • written 17 months ago by aniketd86110
2

Good question. There was a recent interview that had some nice details about the ALT features and other aspects of the new assembly: http://www.bio-itworld.com/2013/4/22/church-on-reference-genomes-past-present-future.html

ADD REPLYlink written 17 months ago by Mary10k
5
gravatar for deanna.church
17 months ago by
deanna.church930
Bethesda, MD
deanna.church930 wrote:

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.

ADD COMMENTlink written 17 months ago by deanna.church930
1

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 ] ?

ADD REPLYlink written 17 months ago by aniketd86110
1

I have also used the GSNAP aligner, seems to be able to account for the alt loci too and it has been published: http://bioinformatics.oxfordjournals.org/content/26/7/873.abstract

However, it does seems like it is focusing more on RNA alignment.

You can find the programme here: http://research-pub.gene.com/gmap/

ADD REPLYlink modified 17 months ago • written 17 months ago by Sam1.4k

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

ADD REPLYlink written 17 months ago by deanna.church930
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