Inputs and Parameters

NanoVar inputs

Mandatory postional arguments

• Long-read FASTQ/FASTA file or mapped BAM file
• Reference genome in FASTA format (e.g. GRCH38 Human reference genome hg38)
• Working directory

Recommended arguments

• Coordinate exclusion BED file (See parameter -f below)

NanoVar options

Usage:

nanovar [-h] [-x ont/pacbio] [-f file] [-c int] [-l int] [-p float]
        [-a int] [-b int] [-s float] [--homo float] [--hetero float]
        [--debug] [--force] [-v] [-q] [-t int] [--model path]
        [--mm path] [--st path]
        [FASTQ/FASTA/BAM] [reference_genome] [working_directory]


Example:
        nanovar -t 24 reads.fa hg38.fa ./work_dir

Positional arguments:

Parameter	Argument	Comment
[FASTQ/FASTA/BAM]	reads.fq/reads.bam	Path to long reads or mapped BAM file. Formats: fasta/fa/fa.gzip/fa.gz/fastq/fq/fq.gzip/fq.gz or .bam
[reference_genome]	hg38.fa	Path to reference genome in FASTA. Genome indexes created will overwrite indexes created by other aligners (e.g. bwa)
[working_directory]	./work_dir	Path to working directory. Directory will be created if it does not exist

Optional arguments:

Parameter	Argument	Comment
-h, --help	-	show this help message and exit
-x, --data_type	ont or pacbio	Type of long-read data - Oxford Nanopore (ont) or Pacific Biosciences (pacbio) [ont]
-f, --filter_bed	path	BED file with genomic regions to be excluded. (e.g. telomeres and centromeres) Either specify name of in-built reference genome filter (i.e. hg38, hg19, mm10) or provide FULL path to own BED file. [None]
-c, --mincov	INT	minimum number of reads required to call a breakend [2]
-l, --minlen	INT	minimum length of SV to be detected [25]
-p, --splitpct	FLOAT	minimum percentage of unmapped bases within a long read to be considered as a split-read. 0.05<=p<=0.50 [0.05]
-a, --minalign	INT	minimum alignment length for single alignment reads [200]
-b, --buffer	INT	nucleotide length buffer for SV breakend clustering [50]
-s, --score	FLOAT	score threshold for defining PASS/FAIL SVs in VCF. Default score 1.0 was estimated from simulated analysis. [1.0]
--homo	FLOAT	Lower limit of a breakend read ratio to classify a homozygous state. i.e. Any breakend with homo<=ratio<=1.00 is classified as homozygous [0.75]
--hetero	FLOAT	Lower limit of a breakend read ratio to classify a heterozygous state. i.e. Any breakend with hetero<=ratio<homo is classified as heterozygous [0.35]
--debug	-	run in debug mode
-v, --version	-	show version and exit
-q, --quiet	-	hide verbose
-t, --threads	INT	number of available threads for use [1]
--model	path	specify path to custom-built model
--mm	path	specify path to 'minimap2' executable
--st	path	specify path to 'samtools' executable

• Removed options after v1.5.0: --force, --mdb, --wmk, --hsb