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Inputs and Parameters
ChengYong Tham edited this page Sep 8, 2023
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- Long-read FASTQ/FASTA file or mapped BAM file
- Reference genome in FASTA format (e.g. GRCH38 Human reference genome hg38)
- Working directory
- Coordinate exclusion BED file (See parameter -f below)
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