This tool is used to detect structural variants from a BAM file using local assembly.
usage: FirstSV V 0.02 [-h] --bamfile bamfile --outputdir outdir --sampleid
sampleid --configinfo config_file
[--targetregion targetregion]
[--bpthreshold bpthreshold] [--spthreshold spthreshold]
[--mpthreshold mpthreshold] [--hard_filter hard_filter]
This tool is used to detect structural variants from a BAM file using local
assembly.
optional arguments:
-h, --help show this help message and exit
--bamfile bamfile, -b bamfile
BAM file created by BWA or other alignment software.
--outputdir outdir, -o outdir
Output direction for results.
--sampleid sampleid, -i sampleid
Sample ID.
--configinfo config_file, -c config_file
Config file direction.
--targetregion targetregion, -r targetregion
Detect Region.
--bpthreshold bpthreshold, -p bpthreshold
Breakpoint Mini Distance.
--spthreshold spthreshold, -s spthreshold
Breakpoint Mini Support Counts.
--mpthreshold mpthreshold, -m mpthreshold
Mini Mapping Quality.
--hard_filter hard_filter, -f hard_filter
Weather to using hard filter.(EXPERIMENTAL)
python FirstSV.py -c config.txt -o /PATH_OF_OUTPUT -i SAMPLE_ID -b BAM_FILE- Standalone BLAT v. 36x1
- samtools-1.3
- bwa-0.7.13
fermi_las was based on the https://github.com/lh3/fermi-lite created by LiHeng.