Liftover bam from custom amplicon to hg19

[anna_vt]

Hi,

I have been aligning sequences to a small subset of hg19 as the project is a custom amplicon.
Is there any tool for converting the bam files aligned to the custom genome to the full hg19?

I guess I could create a custom liftover chain file and then use crossmap to liftover.
Has anyone else done this or similar?

Cheers

[wdecoster]

The least biased and most correct way would be to repeat the mapping to the full genome. As far as I know, it's not advisable to map to a small subset of the genome since you might be "forcing" the aligner to chose the "best" mapping site which may not be the correct one.