Question: Grch38 And Reference Alignment
gravatar for aniketd86
19 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 • 1.8k views
ADD COMMENTlink modified 19 months ago by deanna.church970 • written 19 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 19 months ago by Mary10k
gravatar for
19 months ago by
Bethesda, MD
deanna.church970 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 19 months ago by deanna.church970

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 19 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 19 months ago • written 19 months ago by Sam1.4k

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

ADD REPLYlink written 19 months ago by deanna.church970
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