I extracted some reads from a region (~200kb) of interest (including the unmapped ones) and all the pairs of unmapped reads from my WGS BAM: I'd like to know if it is possible to automatically (using vg?) detect any structural variant using the spades assembler (http://cab.spbu.ru/files/release3.12.0/manual.html ) for this region of interest .
The output directory looks like:
assembly_graph_after_simplification.gfa assembly_graph.fastg assembly_graph_with_scaffolds.gfa before_rr.fasta contigs.fasta contigs.paths corrected dataset.info input_dataset.yaml K21 K33 K55 K77 misc params.txt pipeline_state run_spades.sh run_spades.yaml scaffolds.fasta scaffolds.paths spades.log tmp
is there any way to automatically detect any large inversion/insertion/deletion/etc.. from the assembly graph ?