I have a question about vg giraffe

[pioneer-pi]

Hello, I use vg giraffe to map reads to pangenome.giraffe.gbz and get map.gam. I check map.gam and find it's different with the result of gam file which map use vg map. Some tags are different. And I have two questions:

1. I check the result of *.gam with vg giraffe, I can't find the information about which chr this read map to? If I want to extract reads which mapping to chr1 from map.gam file. There is no xg file.How should I do?
2. If I want to use the map.gam file to augment the org vg graph.(Like vg augment -x *.xg -A *.gam *.gam > *_aug.vg). Can I use this function with vg giraffe

[jeizenga]

If you are mapping to a graph in which chromosomes correspond to connected components in the graph, you can split the GAM into chromosome-wise GAMs with vg chunk -C -P. GAMs from vg giraffe should work the same in vg augment as GAMs from vg map, as long as you are augmented a graph with equivalent node IDs.

[pioneer-pi]

Thank you. There is another question. If I wanna do Whole genome read mapping using vg giraffe. So I get the whole_genome.giraffe.gbz, whole_genome.dist and whole_genome.min.
Now I want to extract a variation graph of specific chr(like chr20 or others) from whole_genome.giraffe.gbz. Because I wanna use the result of read mapping from vg giraffe to augment the giraffe and get the specific region.

[xchang1]

vg chunk can be used to find a subgraph of a graph as well. You can use it with -x whole_genome.giraffe.gbz -C -P as with the GAM, and it will output the subgraph.

[pioneer-pi]

@xchang1 Thank you! I get it. But there is a confusion about the gam result of vg giraffe. Compared with the gam result of vg map, there are some different tags. A tag called "refpos" is missing. I guess the meaning of this tag is mapping position of read. So can I keep this tag with vg giraffe

[xchang1]

You can use vg annotate to annotate the mapped reads with the positions that they overlap the reference on the graph.

Depending on what you're using it for, it might be better to use vg surject to convert the gam file to a bam/sam file. surject will try to project the alignment onto the linear reference, so it will produce a better alignment to the reference than just using annotate to find the overlap