Graph Alignment Format in vg

For full documentation, see https://github.com/vgteam/vg/blob/master/doc/static/GAF.md.

A lot of the information in a Graph Alignment Format file is encoded in tags. To interpret the file you need to know what each tag means.

Many tags are documented in the minimap2 man page; when vg emits one of those tags, is generally follows that.

To ensure that read sequences are recoverable, vg uses a minimap2-style cs tag to encode a "difference string", instead of the cg CIGAR string tag.

Here are some particular tags vg supports:

Shared with minimap2:

• AS: Alignment score from dynamic programing
• dv: Divergence

Newly invented:

• bq: Base qualities
• pd: Properly paired flag, by Xian
• fn: Next fragment in pair
• fp: Previous fragment in pair