Description of variations of and extensions to the alpha version
|POS||comma-separated list with the position(s) of each variant impacting the splice site|
|ID||comma-separated list with the ID(s) of each variant impacting the splice site (same ordering as in POS)|
|REF||comma-separated list with the reference string of each variant impacting the splice site (same ordering as in POS)|
comma-separated list with the variant string of each variant in single (same ordering as in POS)
A comma-separated list of the variants (and all info deferred from them) can lead to ambiguous results if one of the variants already describes multiple alternatives, e.g.
... rs6040355 A G,T ...
... microsat1 GTCT G,GTACT ...
as provided as examples on the VCF definition page.
comma-separated list of the quality for the corresponding assertions in ALT
Possibly ambiguous in the case of variants with multiple alternatives, as above.
comma-separated list whether the variant position has passed the filtering
As long as there is only one value per variant/SNP, and not per alternative/ALT, then there should be no problem.
MOD: either alternative (ALT) or constitutive (CON) splice site
VARx: (combinations of) variants that form each alternative variant (same ordering x as in other columns POS, ALT, ...)
SEQ: splice site sequence(s) for the reference and all variants applied described by the VARx attributes
SCORE: comma-separated list of first the score of the reference site, and then of all variants in the usual ordering