which haplotypes were saved in .gbz file?

Question

[chuanj8848]

How to know which haplotypes/assembly IDs were used in a .gbz file?

Is there anyway to visualize a .gbz file ? just like samtools view .bam file

In addition, does .gbz file contain more information compared with a .gfa file?

Thank you very much.

Answer 1

[Jouni Sirén]

You can display metadata on all paths in the graph using vg paths -M -x graph.gbz. If you want to list sample or contig names, you can use vg gbwt -S -L -Z graph.gbz and vg gbwt -C -L -Z graph.gbz, respectively.

Graph visualization is a complex topic, and the answer depends on the specifics of the data you have and what you want to achieve with the visualization.

A GBZ file is mostly equivalent to a subset of GFA, as described in the paper. It can also store arbitrary metadata as key-value pairs, but nobody is really using this functionality at the moment. It may also store a translation between two equivalent representations of the graph: GFA (segments with string names storing sequences of arbitrary length) and vg (nodes with integer identifiers storing short-to-medium sequences).