I am inspired by the article: https://jmonlong.github.io/manu-vggafannot/. I am not working well with gam format. So I am thinking about build a pipline based on …

Hi, I am trying to get alignment stats from a gaf file using vg stats -a <gaf> and got a long error. May I ask …

Hi everyone, I am dealing with gam file format and trying to understand its structure. I convert my gam files to JSON using vg. I …

In linear reference(sam,bam) or in pangenomic alignment(gam,gaf), is it possible to a read that is aligned twice or more? Can we observe that a read …

Hi everyone, I dont understand what the optional strings at the end lines of paf and gaf files really mean? [This link][1] and [this link][2] …

Hi everyone, I am trying to understand pangenomic data/file formats. In the vg's descripton of file format, it says gam is similar to sam/bam and …

When I use `vg convert` (v.1.39) to convert a `gam` file to a `gaf` file (or vice versa), I find that the order of the …

Hello! I'm trying to get multiple alignments with their corresponding **alignment scores** for paired-end reads against a pangenome using `vg giraffe`, and then `vg surject` …

I noticed it is now possible to output alignments in gaf files instead of gam, which is great! How difficult would it be to convert …

<p>I am trying to convert the output of blast in a .sam or .bam file. I tried to use the blast2sam tool but there are …