incorporating variant calling with novel transcript discovery

[jv-20]

Description of feature

Thanks for the pipeline. it would be great if PSQAN can be incorporated into the workflow and combining the variant calling functionalities of https://github.com/genomic-medicine-sweden/nallo.

[nadjano]

Hi,

thank you for your suggestions! Unfortunately, we are not planning to incorporate any variant calling functionalities as it is out of scope of this pipeline. The pipeline is part of a framework for allele-specific expression analysis where we expect as a input a reference genome that is already haplotype resolved.