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Description
The dbNSFP annotation set will in some cases have values for all or only a subset of the known transcripts. Is there a way to limit retrieval of annotations to a single transcript, or to predict the order of the lists?
For example, for the variant NM_000546.6(TP53):c.833C>G I would like the REVEL and Alphamissense annotations. From the dbNSFP data set we can see the these annotations are available only a different subset of the transcripts - see attached text file dbNSFP_query.txt
I can use this query to retrieve the values:
https://myvariant.info/v1/variant/chr17:g.7673787G%3EC?assembly=hg38&fields=dbnsfp.revel,dbnsfp.alphamissense,dbnsfp.ensembl.transcriptid
But the output lists have 19 values (transcripts), 16 values (alphamissense.score) and 6 values (revel.score), without an obvious order:
{
"_id": "chr17:g.7673787G\u003EC",
"_version": 2,
"dbnsfp": {
"_license": "http://bit.ly/2VLnQBz",
"alphamissense": {
"score": [0.9936, 0.9899, 0.9873, 0.9932, 0.9907, 0.9848, 0.9852, 0.9966, 0.9951, 0.9944, 0.9947, 0.9952, 0.9968, 0.9941, 0.9921, 0.9911]
},
"ensembl": {
"transcriptid": [
"ENST00000359597",
"ENST00000504290",
"ENST00000510385",
"ENST00000504937",
"ENST00000619186",
"ENST00000618944",
"ENST00000610623",
"ENST00000610292",
"ENST00000269305",
"ENST00000620739",
"ENST00000617185",
"ENST00000455263",
"ENST00000420246",
"ENST00000622645",
"ENST00000610538",
"ENST00000445888",
"ENST00000619485",
"ENST00000615910",
"ENST00000509690"
]
},
"revel": {
"score": [0.951, 0.951, 0.951, 0.951, 0.951, 0.951]
}
}
}
If I want values only for ENST00000269305 (the 9th item in the list) is there a way to limit the search to only that transcript? Alternatively (and ideally) could the list order be maintained with empty fields e.g:
"score": [0.951,0.951,0.951,0.951,0.951,.,.,.,0.951,.,.,.,.,.,.,.,.,.,]