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?
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gulin201909 •
1 answer
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.
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