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C,G 29,3PASS,q-1000SSID=-14370^20;MOD=ALT;VAR1=SNP1;VAR2=SNP2;SEQ=



Description of variations of and extensions to the alpha version

POScomma-separated list with the position(s) of each variant impacting the splice site
IDcomma-separated list with the ID(s) of each variant impacting the splice site (same ordering as in POS)
REFcomma-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

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