The α-format described here has been applied to describe the splice site variants of the Geuvadis Project.
| CHR | POS | ID | REF | ALT | QUAL | FILT | INFO | FORMAT | I1 | I2 |
|---|---|---|---|---|---|---|---|---|---|---|
| 20 | 14370 | -14370^20 | TTGTACGTG | ttgtaGgtg,ttgtCcgtg | -10001 | q-1000 | MOD=ALT;ALT1=SNP1;ALT2=SNP2;VAR_SCORES=1.5277311,3.4223458;SNPS=SNP1,SNP2 | GT | 0|1 | 0|0 |
| ... |
Description of variations of and extensions to the standard VCF
| Attribute | Description |
|---|---|
| POS | the position of the splice site, provided as the first/last position included in the adjacent exon (cf. AStalavista default coordinates) |
| ID | string identifying the splice site uniquely, composed by strand, genomic coordinate, site type symbol (cf. AStalavista conventions) and chromosome ID |
| REF | the reference sequence of the splice site, as obtained by extracting the corresponding sequence stretch from the genome |
| ALT | comma-separated list of the corresponding splice site sequences after applying the corresponding genetic variant(s) to the reference sequence |
| QUAL | the score of the reference splice site sequence (as shown in REF) |
| FILT | "q-1000" when the splice site sequence has not observed in the training set (-Infinity, in practice represented by a value << -1000), "PASS" otherwise |
| INFO | MOD: either alternative (ALT) or constitutive (CON) splice site ALTx :(combinations of) variants that form each alternative variant (same ordering as in ALT column) VAR_SCORES: comma-separated list of scores assigned to the corresponding variant(s); the ordering corresponds to the one used for ALT SNPS: concatenation of all variants considered for the description of this splice site (line) |