I want to convert the GAM to BAM format via VG surject command, but it failed because of the different attributes between GraphAligner and vg aligner. The differences are shown below:
VG aligner:
GraphAligner:
It looks like vg surject uses node_id for conversion, and this node_id is the one in the GFA graph. Here, GraphAligner assigns a different value to node_id, as a result, the error shows Attempted to get handle for node 2797 not present in graph.
I am wondering if it convenient for you to change the output format, so that it is compatible with VG's GAM.
Dear developer,
I want to convert the GAM to BAM format via VG surject command, but it failed because of the different attributes between GraphAligner and vg aligner. The differences are shown below:
VG aligner:
GraphAligner:
It looks like vg surject uses
node_id
for conversion, and thisnode_id
is the one in the GFA graph. Here, GraphAligner assigns a different value tonode_id
, as a result, the error showsAttempted to get handle for node 2797 not present in graph
.I am wondering if it convenient for you to change the output format, so that it is compatible with VG's GAM.
Best, Jiadong