indels

[RafaFariasVarona]

Hi! In the vcf generated by NanoCaller there are some records that differ from others because they are only defined by ORP (Original variant position), ORL (Original reference length) and GQ (Genotype Probability) instead of GT, DP, VF... What are these records? Are they variants?

[RafaFariasVarona]

I think they are indels. Why NanoCaller doesn't provide the DP (read depth), VF (alternative allele frequency) and AD (allele depth) in these cases?

[umahsn]

Hi! During indel calling, NanoCaller detects all sequence alterations between reference and sample near a candidate indel. As a result, it predicts the complete alternative sequence compared to the reference which may contain multiple indels, multiple SNV and block substitutions near each other. These original indel predictions can be seen in intermediate_indel_files/variant_calls.raw.indel.vcf file. Later, we normalize these complex indels and split them into basic SNVs and indels using RTG-tools vcfdecompose. This step adds ORL and ORP to the signify where the original indel record was.

I will add DP, VF and AD to indel output as well, thanks for bringing this to our attention.

[RafaFariasVarona]

Thank you for your answer! Will you upload a new NanoCaller version soon that includes these changes?