Hi,
The R package I’m using represents indels using “-” notation and omits the reference base. I’m wondering whether the “chromosome-position-ref-alt” format required by the FAVOR API includes the reference base for indels. How are indels represented?
Best,
Shujie
Yes, achromosome-position-ref-alt format is required in the API. Can you elaborate what you mean by reference base with an example?
I mean my data in R only represent indels in a simplified form like (-/TT), instead of showing the complete information like C/CTT.
These patterns are supported in the API; however, our database doesn’t contain instances of such cases directly.
If you’re referring to a simplified form like (-/TT) to match all cases with the alternate allele TT, this is not currently supported but would be a valuable addition to Favor. We can add this.