Versions Compared

Old Version 2

changes.mady.by.user Micha Sammeth

Saved on

compared with

New Version 3

changes.mady.by.user Micha Sammeth

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

CHRPOSIDREFALTQUALFILTINFOFORMATI1I2
2014373,14374

SNP1,SNP2

A,C

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

TTGTACGTG,ttgtaGgtg,ttgtCcgtg;SCORE=-10001,1.5277311,3.4223458

GT0|10|0
...          

...

AttributeDescription
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)
ALT

comma-separated list with the variant string of each variant in single (same ordering as in POS)

Warning

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.

QUAL

comma-separated list of the quality for the corresponding assertions in ALT

Warning

Ambiguous Possibly ambiguous in the case of variants with multiple alternatives, as above.

FILT

comma-separated list whether the variant position has passed the filtering

Note

As long as there is only one value per variant/SNP, and not per alternative/ALT, then there should be no problem.

INFO

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