Tools for integrating the long reads transcriptomic data into reference genome with gaps in specific region

Question

[divinomas]

We want to investigate the epigenomic state of a specific region (several million base pairs) on human chromosome, which is very polymorphic and notoriously difficult to assemble using short reads. We notice that some long reads transcriptomic data but not long reads genomic data are available for this region.

So is there any tool to extract the DNA sequence at all the related polymorphic sites and "patch" the human reference genome with the cell-specific transcriptomic data?

[jean.elbers]

Perhaps you could do SNP/indel calling by aligning the transcriptomic reads with an aligner such as BBMap (maybe using mapPacBio.sh) then calling variants with BBTools' callvariants.sh, then using BCFtools to get the consensus sequence?