I am attempting to extract information from the CSQ annotation for each of my variants.
According to CSQ documentation, "consequences of compound variants which span multiple sites are printed in one record only, the remaining records link to it by '@posistion'". I am hoping to better understand how sites are linked so that I can the full annotation to each variant.
I am struggling to understand the linkage logic, as there appear to be different ways the @posistion linkage is listed in the annotation.
The first pattern I've found appears to make sense with the quote from the documentation:
CH. POS BCSQ annotation
I 10. @26386
As i understand it, the full annotation of the variant at position 10 can be found at position @26386?
The second pattern I have found confuses me a bit more.
CH. POS BCSQ annotation
II 243378 @2862446,@2863936, frameshift | Gene transcript | (rest of annotation)|
Is this the full are these linking to another position with a different annotation or are they listing the components of the compound variant?
This may be a simple question but its been difficult to link each position to an annotation and clearly understanding how bcftools csq links these variants will be extremely useful!
