phasing tumor long-reads

Question

[eesiribloom]

I have already done some asking around but have got contradictory advice...

here and here

I thought it was an interesting point to raise on this forum as others might have a similar issue.

I have nanopore long-reads from tumor (tumor only). I also have SNP/indel variant calls from the same sample from illumina in both germline (normal) and tumor data.

I want to try and get phasing information for the tumor e.g. with whatshap phase

which input.vcf should I use to accompany my tumor.bam?

1. illumina SNP/indel calls from normal
2. illumina SNP/indel calls from
3. tumor nanopore SNP/indel calls from tumor

This manuscript opts for (1). Same here, although their method was more complicated. So I am inclined to go for this method, although there are compelling points for option (2) also (see link above).