Does vg giraffe output secondary and supplimentary alignments?

Question

[lushjia]

I'm using vg giraffe to align short-read sequencing data to a minigraph-cactus pangenome graph. When I checked some repetitive regions, I noticed that reads that could map to multiple locations were only reported once in the resulting .gam file. I also ran vg stats on the .gam file and got:

Total secondary: 0

Does vg giraffe report secondary and supplimentary alignments? Or is there a specific parameter to enable vg giraffe to ouptut secondary and supplimentary alignments?

Answer 1

[Jouni Sirén]

There is option --max-multimaps INT, which makes Giraffe output at most INT alignments for each read. We don't really test it, but it should work. The actual number depends on how many candidate alignments pass earlier filters, such as --max-alignments INT (do tail alignment for this many extended seeds) and --extension-score INT / --extension-set FLOAT (thresholds for doing tail alignment based on scores relative to the best score).

You can find all the hidden options with vg giraffe -h. Most computational parameters can be adjusted, but there is little documentation for them and changes may have unexpected consequences.

[lushjia]

Thank you so much for the information! It's really helpful!