bvc - bifurcation variation detection

Bubble detection using pan-level approach in variation graphs. Reporting variation based on pan-genomix information stored in paths.

Algorithm

Later

Installation

From source

git clone https://github.com/MoinSebi/pan-sv.git
cd pan-sv 
cargo build --release

Running

Help message

bvd 0.1.0

Sebastian V

Bifurcation variation detection

USAGE:
    pan-sv --gfa <gfa>

FLAGS:
    -h, --help       Print help information
    -V, --version    Print version information

Input options:
    -d, --delimiter <delimiter>    Delimiter for between genome and chromosome
    -g, --gfa <gfa>                Input GFA file

Output options:
    -o, --output <output>    Output prefix [default: panSV.output]
        --nestedness         Adds NL-tag (nestedness-level) to the stats output file [default: off]

Threading:
    -t, --threads <threads>    Number of threads [default: 1]

Processing information:
    -q                  No updating INFO messages
    -v <verbose>        -v = DEBUG | -vv = TRACE

If delimiter is set, counting will be according to sample_name (see below) and not the path name.
PanSN-spec: [sample_name][delim][haplotype_id][delim][contig_or_scaffold_name]

Example:

./bvd -g data/testGraph.gfa -o panSV.out

TODO

• More tests for validation
• Check if everything is working accordingly

Output

1. bubbles statistic and
2. BED file for start and end position found in all sequences in the graph Documentation