Merging .gam files

Question

[elizabethmareeross]

Can anyone point me towards a method to merge gam files that are created by using ' vg map ' to map illumina reads to my genome graph? I would like to be able to map all of the sequencing runs separately and then merge the output (something like samtools merge but for a gam) so that I can call SVs for each sample.

Thanks.

Answer 1

[glenn.hickey]

GAM files can be combined with cat. Note that vg call can only genotype one sample at a time, though.

[ernestolowy]

Hi Glenn,

Can you provide an example command on how to do this merge?

Thanks, ernesto