gVCF what is a "break-end replacement"

Question

[Kermit]

As seen in the gVCF documentation by Illumina - what are break-ends in the ALT column?

ALT: Comma-separated list of alternate non-reference alleles called on at least one of the samples.

Options are:

• Base strings made up of the bases A,C,G,T,N

• Angle-bracketed ID String (”<id>”)

• Break-end replacement string as described in the section on break-ends.

https://support.illumina.com/help/BaseSpace_App_WGS_BWA_help/Content/Vault/Informatics/Sequencing_Analysis/BS/swSEQ_mBS_gVCF.htm

I can't find this section on "break-ends"

Answer 1

[Ram]

Here's the VCF format specification document. On page 17, there is a description of how break-ends are represented.

    These 3 elements are combined in 4 possible ways to create the ALT. In each of the 4 cases, the assertion is that s
    is replaced with t, and then some piece starting at position p is joined to t. The cases are:
    REF ALT Meaning
    s t[p[ piece extending to the right of p is joined after t
    s t]p] reverse comp piece extending left of p is joined after t
    s ]p]t piece extending to the left of p is joined before t
    s [p[t reverse comp piece extending right of p is joined before t

[Kermit]

Thanks @RamRS. Do you know if this is actually put into practice in variant calling pipelines?

[Ram]

I'm sorry, I don't really know. It depends on how new this convention is, as well as which tools are used in the pipeline. If GATK 3.7+ says it follows this convention, most pipelines would have it. If only GATK 4 adopted this, then it might not be as widespread. In conclusion, it all depends.