Handling of Reverse Strand in GAM file

Question

[ved_vyas]

In the gam file, for a reverse strand how is the CIGAR string represented? Is the read sequence already in reverse compliment form in gam file and the CIGAR string follows this read seq and the Flag is raised for reverse strand?

Answer 1

[glenn.hickey]

There is some documentation on the GAM format here: https://github.com/vgteam/libvgio/blob/master/deps/vg.proto

Note that in vg we are phasing out GAM in favour of GAF: https://github.com/lh3/gfatools/blob/master/doc/rGFA.md#the-graph-alignment-format-gaf with "cs" cigar tags as defined here: https://lh3.github.io/minimap2/minimap2.html

Most (but not yet all) vg tools have options to input or output GAF instead of GAM