Support for multiallelic variant calls

[lauren-tjoeka]

Hi! It would amazing if you add a feature for multiallelic variant calls. I believe only biallelic calls are currently supported. It would be very useful for cancer samples and I don’t believe a variant caller of this nature currently exists for ONT long read cDNA generated from 10x libraries.

Perhaps this data is already generated but is getting filtered out in lieu of the most abundant alternate allele.

[zhengzhenxian]

Hi @lauren-tjoeka,

Currently, Clair3-RNA primarily supports germline variant calling, which operates under a diploid assumption. As a result, it only outputs biallelic calls. We have not conducted extensive testing on cancer samples due to the lack of available somatic samples in lrRNA-seq. If you have any relevant samples for us to test, we would greatly appreciate the opportunity to evaluate them. Thank you.

Zhenxian