Variant annotation failing

[Chelsea-Na]

We have MAF data that is failing annotation with genome nexus (see example.csv). We are wondering why it is failing?

• Please see an example input: example.csv

To provide more context, we had recently removed some logic before annotating with genome-nexus. The logic was if the ref allele and alt allele do not match and if the first char of the ref allele is the same as the first char alt allele, then we remove the first char of both alleles and shift the start position forward by 1.

Using the example file provided, the logic would update the start_position from 25398284 to 25398285, the reference allele from CC to C and the alt allele from CG to G. Then genome-nexus would annotate the variant with KRAS. However, after removing the logic, genome-nexus fails to annotate this variant.

[Chelsea-Na]

Here are more examples that fail annotation: more_examples.csv