We have been experimenting with VEP (Variant Effect Predictor). One of the meta data attributes that we are interested in is the SIFT score, indeed when we apply the dbNSFP plug we get a column containing the scores (named SIFT_score). However, I don't understand why there are sometimes dots or multiple values in the fields. For example, the gene ENSG00000196924 below has 5 transcripts:
The SIFT_score column contains several values, not 1 per transcript/rs-number...
Here is another example that confuses me (I added the SIFT_pred column this time):
There are two mutations, the lower one can be expressed in 4 transcripts and I thus understand that there can be 4 SIFT scores, but why are all for in given in every row? Is the first one the SIFT_score for the first transcript?
One last example, again 4 transcripts, but now 2 of the scores are dots, what does that mean?
I have been looking for quite some time now how to interpret this data, any help is appreciated.