Generates haplotype plots from VCF files.
Project description
Haplotype plot
Generates haplotype plots for VCF files. Requires Python 3 to run.
Usage
usage: main.py [-h] -v VCF [-o OUTPUT] -c CHR -p PARENTAL [--version]
[-z {HOM,HET}] [--conf KEY=VALUE [KEY=VALUE ...]]
Creates a haplotype plot from a VCF file
optional arguments:
-h, --help show this help message and exit
-v VCF, --vcf VCF path to the input VCF file
-o OUTPUT, --output OUTPUT
path to the output PNG haplotype plot file
-c CHR, --chr CHR chromosome to plot from the VCF
-p PARENTAL, --parental PARENTAL
sample name from the VCF used as parental haplotype
--version show program's version number and exit
-z {HOM,HET}, --zygosis {HOM,HET}
zygosis of the input VCF file
--conf KEY=VALUE [KEY=VALUE ...]
set a number of key-value pairs to modify the default
plot configuration (do not put spaces before or after
the = sign). Possible values are: 'start=integer',
'end=integer'. If a value contains spaces, you should
define it with double quotes: foo="this is a
sentence".
For examples of use please go to the documentation.
Project details
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haplotype_plot-1.0.1.tar.gz
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