Hello all,

I am trying to extract node coverage information from .gam files and it seems that vg pack can do that. However, using the following command

vg pack -x {input.graph} -g {input.gam} --as-table > {output}

I get a file like this:

seq.pos node.id node.offset coverage
529 6416803 0   74
530 6468162 0   0
531 6323978 0   2
532 6465270 0   1
533 6465270 1   1
534 6465270 2   1
535 6465270 3   1
536 6465270 4   1
537 6465270 5   1
538 6465270 6   1
539 6465270 7   1

where you have several time the same node with different node.offset. I have therefore two questions: To what exactly corresponds the node.offset column ? And is there a way to simply obtain the number of reads that map to each node (like what gafpack seems to do; or what you get when doing vg pack but on edges) using vg ?

Thanks in advance for taking the time to read this, Best!