Please install python3 and following module first: scipy，numpy，configparser and PyVcf.
NaSV was built based on LAST mapping data.LAST mapping LAST is able to map the reads in non-overlapping split segments.LAST can be download as the zip file from http://last.cbrc.jp/, and installed by following comands:
> gunzip last.zip
> cd /path/to/lastdir
> make
First you need to index your reference genome by creating a lastal database:
> lastdb [referencedb] [reference.fa]
Train LAST to get the best scoring parameters for your particular alignment. We typically use a subset of > 10,000 reads for this step:
> last-train -Q1 [referencedb] [reads_sample.fastq] > [my-params]
Map your fastq data to reference:
> lastal -Q1 -p [my-params] [referencedb] [reads.fastq] | last-split > [reads.maf]
All of the above commands can also be run at once using pipes:
> lastal -Q1 -p [my-params] [referencedb] [reads.fastq] | \
> last-split > [reads.maf]
NaSV usage
> NaSV.py [-h] [-c CONFIG] [-o OUTPUT] [-i reads.maf]
NaSV arguments and parameters:
required arguments:
-i, --maf : /path/to/reads.maf
-o, --output : Give the full path to the output vcf file
optional arguments:
-h, --help : Show the help message and exit
-c, --config : Give the full path to your own ini file [ default: config.ini ]
optional configuration parameters: Nasv uses a config.ini file which contains default settings for all running parameters. Users can change the parameters by creating their own config.ini file and provide this as a command line argument [-c]
**Reads segments options:**
**[Filter options]**
*Minimum mapping quality of the segment*
mq_cutoff=10
*Maximum percentage of unaligned first bases for a qualified read*
start_cutoff=0.2
**Parameters for tuning detection and clustering of breakpoints:**
**[Detection options]**
*Minimum number of breakpoint-junctions (i.e. split-read junctions) for clustering*
read_cutoff=5
*Maximum distritution distance for a breakend position (assuming normal distribution)*
merge_bp_cutoff=100
*Maximum distance for two breakend positions decided as homology*
merge_cutoff=20
**Parameters for setting the FILTER flag in the vcf output:**
**[Output filter options]**
*Minimum reads percentage for a breakpoint decided as precise*
precise_cutoff=0.5