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Inputs and Parameters
Tham Cheng Yong edited this page Mar 4, 2020
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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] [-f FILTER_BED] [-l MINLEN] [-p SPLITPCT] [-a MINALIGN]
[-b BUFFER] [-s SCORE] [-v] [-q] [-t [1-54]] [--force]
[--mdb MDB] [--wmk WMK] [--hsb HSB]
[long_reads] [reference_genome] [working_directory]
Example:
nanovar -t 24 reads.fa hg38.fa ./work_dir
Positional arguments:
Parameter | Argument | Comment |
---|---|---|
[long_reads] | reads.fa | Path to long reads. Formats: fasta/fa/fa.gzip/fa.gz, fastq/fq/fq.gzip/fq.gz |
[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 |
---|---|---|
-f, --filter_bed | bed_file | 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] |
-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 derived from simulated analysis. [1.0] |
--mdb | mdb_path | Specify path to 'makeblastdb' executable |
--wmk | wmk_path | Specify path to 'windowmasker' executable |
--hsb | hsb_path | Specify path to 'hs-blastn' executable |
-t, --threads | INT | number of available threads for use [1] |
--force | - | run full pipeline, do not skip any redundant steps (e.g. index generation) |
-q, --quiet | - | hide verbose |
-h, --help | - | show this help message and exit |
-v, --version | - | show version and exit |