Subset a GAM (graph alignment) file
I would like to subset a GAM file to contain less reads so I can visualize it with Sequence Tube Map.
I've tried
vg view -a myreads.gam | head -n1000 | vg view -G -J
but it doesn't recognize the standard input.
I was hoping that something like samtools view -s 0.1 bamfile.bam
Thanks
1 answer
For the first 1000 reads:
vg view -a myreads.gam | head -n1000 | vg view -a -G -J - > myreads_1000.gam
For downsampling like samtools
vg filter myreads.gam -d 0.1 > myreads_0.1.gam
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