Calling large gaps in small contigs

[cgroza]

Hi,

I have somewhat short contigs in the range of 8 to 15 kbp. These contigs contain a 6 kbp insertion and are surrounded by 1 to 4 kbp of flanking reference sequence on each side. I wish to use minimap2 to align the contig to the reference locus and call the L1 insertion. The problem is that minimap2 splits the alignment where the L1 insertion begins and does not call the insertion, only giving the matches for the flanks.

How do I tune minimiap2 to call large gaps surrounded by small flanks? I am using the C++ bindings of minimap2 and I can control every parameter directly.

My thanks, Cristian

[cgroza]

Here is an example if it helps. It contains a 6kb insertion surrounded by 4kbp flanks and I wish to map it to a reference region that is 8kbp long. example.fa.gz

Cristian

[cgroza]

Also, if it helps, here is the dotplot with the target region (y-axis) and the contig with the insertion (x-axis). As we can see, there is a large gap in the middle I would like minimap2 to call.

Thank you for any clue!