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Is there any existing tool which can calculate how many reads are mapped in .gam file which is generated by command:
for example the .gam file is "graph.read.gam"
You can get some basic statistics about the GAM file with vg stats -a alignments.gam [graph-name]. The graph file is optional, but if you include it, vg stats will compute some extra statistics.
vg stats -a alignments.gam [graph-name]
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