search

vgteam / vg

tools for working with genome variation graphs
https://biostars.org/tag/vg/
Other
1.07k stars 191 forks source link

vg giraffe output file #4247

Closed Kled111 closed 3 months ago

Kled111 commented 3 months ago

I want to align a fastq file to a pangenome file. I used the following command: vg giraffe -Z pg.gbz -d pg.dist -m pg.min -p -t 64 -f xxx.fastq > out.gam

I found the vg giraffe --help command indicates that the default output is a GAM file。

But when I try to "less out.gam", it turned to be a binary file. Is this normal？What is the format of this output file？

My vg version is "vg 1.55.0 - Bernolda", and I use the binary file in this url: https://github.com/vgteam/vg/releases/download/v1.55.0/vg

glennhickey commented 3 months ago

This is normal. GAM is binary. You can view it with vg view -a or vg convert -G

https://github.com/vgteam/vg/wiki/File-Formats#gam-graph-alignment--map-vgs-bam