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

I came across a slide share about the new GRCh38 assembly and its ALT_LOCI assemblies. (

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 (

Nice overview of ALT LOCI in GRCh38 (Will GRC38/HG20 be a multiple sequence reference genome?)

thanks in Advance,


alignment human • 2.2k views
ADD COMMENTlink modified 23 months ago by deanna.church990 • written 23 months ago by aniketd86110

Good question. There was a recent interview that had some nice details about the ALT features and other aspects of the new assembly:

ADD REPLYlink written 23 months ago by Mary11k
gravatar for
23 months ago by
Bethesda, MD
deanna.church990 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 23 months ago by deanna.church990

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 23 months ago by aniketd86110

I have also used the GSNAP aligner, seems to be able to account for the alt loci too and it has been published:

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

You can find the programme here:

ADD REPLYlink modified 23 months ago • written 23 months ago by Sam1.7k

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

ADD REPLYlink written 23 months ago by deanna.church990
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 444 users visited in the last hour