Multiple entries for the same variant in custom databases
algarsi3 opened this issue · 1 comments
algarsi3 commented
I need to create a custom database where a variant can have zero, one, or many annotations.
For instance, I need an output like this:
{
...
"variants": [
{
"vid": "17-7125299-C-T",
"chromosome": "chr17",
"begin": 7125299,
"end": 7125299,
"refAllele": "C",
"altAllele": "T",
"my_db": [
{
"significance": "resistance",
"disease": "colorectal cancer",
"direction": "supports",
},
{
"significance": "sensitivity response",
"disease": "ovary adenocarcinoma",
"direction": "supports",
},
]
...
}
I tried creating a tsv file with duplicated entries, which threw an error. I can generate a custom database that leads to the following annotation:
{
...
"variants": [
{
"vid": "17-7125299-C-T",
"chromosome": "chr17",
"begin": 7125299,
"end": 7125299,
"refAllele": "C",
"altAllele": "T",
"my_db": {
"significance": "resistance|sensitivity response",
"disease": "colorectal cancer|ovary adenocarcinoma",
"direction": "supports|supports"
},
...
}
However, this is not what I would like to achieve. Could you help me achieve the desired output? This output is similar to the "transcripts" annotations, but I cannot see how to generate such custom databases in the documentation.
Thank you.
algarsi3 commented
Hello, would you be able to help me with this?