Bubble detection using pan-level approach in variation graphs. Reporting variation based on pan-genomix information stored in paths.
##Installation
From source
git clone https://github.com/MoinSebi/pan-sv.git
cd pan-sv
cargo build --release
Help message
panSV 0.1.0
Sebastian V, Christian K
Bubble 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]
./pan-sv -g data/testGraph.gfa -o panSV.outTODO
- More tests for validation
- Check if everything is working accordingly
- bubbles statistic and
- BED file for start and end position found in all sequences in the graph Documentation
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