Under development
| CHR | POS | ID | REF | ALT | QUAL | FILT | INFO | FORMAT | I1 | I2 |
|---|---|---|---|---|---|---|---|---|---|---|
| 20 | 14373,14374 | SNP1,SNP2 | A,C | C,G | 29,3 | PASS,q-1000 | SSID=-14370^20;MOD=ALT;VAR1=SNP1;VAR2=SNP2;SEQ= TTGTACGTG,ttgtaGgtg,ttgtCcgtg;SCORE=-10001,1.5277311,3.4223458 | GT | 0|1 | 0|0 |
| ... |
Description of variations of and extensions to the alpha version
| Attribute | Description |
|---|---|
| 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) |
| ALT | 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. |
| QUAL | comma-separated list of the quality for the corresponding assertions in ALT Possibly ambiguous in the case of variants with multiple alternatives, as above. |
| FILT | 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. |
| 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 |
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