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.
I can't find this section on "break-ends"
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
Thanks @RamRS. Do you know if this is actually put into practice in variant calling pipelines?
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.
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