IGV - is it possible to tell what allele a read is from?

Question

[amy__]

Hello,

Does anyone know if it is possible to work out which allele a read is referring to in IGV? For example, if I have a heterozygous variant, is it possible to work out which allele it is likely coming from - is there a way to work that out from the reads in the bam file?

Such as this insertion for example? I assume not, but just wanted to ask.

Thanks! Amy!

Answer 1

[barslmn]

Deciding the origin of an allele is called variant phasing. We can make this decision by observing the variant with other nearby variants. We call chunk of these variants inherited together from a parent a haplotype. There are also tools which can be used to phase variants (haplotype estimation). These tools can estimate haplotypes or impute unknown genotypes by using already phased datasets like 1kg and hapmap projects.

It's one of the limitations in methods where we're fragmenting the DNA like short read sequencing or SNP array. Talking about sequencing; when we are looking at small reads (i.e. 70-150 bp) we can't determine where the allele comes from because we don't have the contextual information of nearby variants. In practice best way to phase a variant is to also sequence the parents (trio sequencing =parents and proband=).

In your example you have a heterozygous variant meaning it is inherited from a parent, but you can't know which one before genotyping the parents for that location.

Examples

Let's say A, B are variants in a gene you're interested in and want to know if they're inherited from the same parent (cis) or one from each parent (trans). You predict A and B variants both cause loss of function (LOF) and knowing if these variants are in the same copy or two separate copies important. If they're trans (each inherited from a different parent) your proband won't have a healthy copy and will be compound heterozygous for that gene. If they're both from the same parent your proband will have a healthy copy.

Example 1

=Only proband no parents=

You can't comment on if the variants are inherited from the same parent or whether which parent they're inherited from.

Proband
   ----------A--------    ……… -----------B-------
    ---------A---------   ………  ----------B--------
     -------------------  ………   -------------------
      ------------------- ………    -------------------

Example 2

=Trio sequencing variant are far away=

You can distinguish which variant is inherited from which parent.

Parent 1                   | Parent 2
   ----------A--------     |  -----------B-------
    ---------A---------    |   ----------B--------
     -------------------   |    -------------------
      -------------------  |     -------------------
                           |
-------------------------------------------------------
Proband
   ----------A--------    ……… -----------B-------
    ---------A---------   ………  ----------B--------
     -------------------  ………   -------------------
      ------------------- ………    -------------------

Example 3

=Variants are close enough to be seen in the same reads=

You can distinguish they're inherited from separate parents but can comment on which parent.

   ----------A--------
    ---------A---------
     --------A----------
      -------A-----------
       -----------B-------
        ----------B--------
         ---------B---------
          --------B----------

[amy__]

Amazing, thank you lots! I did suspect that