“chromosome-position-ref-alt“ format for indels

Functional Annotation Database
1

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

2

Yes, achromosome-position-ref-alt format is required in the API. Can you elaborate what you mean by reference base with an example?

3

I mean my data in R only represent indels in a simplified form like (-/TT), instead of showing the complete information like C/CTT.

4

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.

5

Thank you! Do you mean favor database doesn’t contain indels currently or doesn’t support the simplified form right now? The simplified form here takes the (ref/alt) from vcf file and deletes the common base. I attach the code here if this helps: #####################################################

Define function to correct indel alleles

#####################################################
def set_alleles(a1, a2):
if len(a1) == 1 and len(a2) == 1:
a1_n = a1
a2_n = a2
elif len(a1) == 1 and len(a2) > 1:
a1_n = “-”
a2_n = a2[1:]
elif len(a1) > 1 and len(a2) == 1:
a1_n = a1[1:]
a2_n = “-”
elif len(a1) > 1 and len(a2) > 1:
a1_n = a1[1:]
a2_n = a2[1:]
return(a1_n, a2_n)

6

Yes, we do not support simplified form as of now.