I am inspired by the article: https://jmonlong.github.io/manu-vggafannot/. I am not working well with gam format. So I am thinking about build a pipline based on gaf format for variant call and more analysis based on graph alignment. Since my gaf file is pretty big, I use gzip to turn it into gz format. I am wondering it can be the input of vg pack and gamsort?
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gulin •
1 answer
Both subcommands can read gzip-compressed GAF files. More generally, vg uses HTSlib file I/O for reading GAF, so any compression option supported by HTSlib will be supported.
Also, it's a good idea to use bgzip instead of plain gzip with large files. bgzip can use multiple compression threads for speed, and the output can be indexed for various applications with tabix.
vg gamsort sorts GAF lines individually. Everything stored in the alignment records is preserved, while any information that may have been encoded implicitly in the order of the alignments will be lost.
You can find a specification of the GAF vg outputs at: https://github.com/vgteam/vg/blob/master/doc/static/GAF.md
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