Removing PCR duplicates in gam file

Question

[gulin201909]

I am using vg giraffe to map my 150bp short read to HPRC pan-genome graph. The results is in gam file. I want to keep information of the graph features in the result so I am developing some scripts based on gam file or tsv after vg filter. I am wondering is there any existing tools for removing PCR duplicates in gam file? If not ,is there any convenient way to achieve this?

Answer 1

[colindaven]

You can have a look at the GAF alignment format which might be a sucessor to GAM, see here - https://github.com/colindaven/awesome-pangenomes?tab=readme-ov-file#file-formats

I have not found GAMs that easy to work with so far, but prefer to use vg surject to get back to the more familiar and well supported BAM file type.