improvar generates fake VCF files using another VCF as a template. This is useful for generating
test data in bioinformatics situations. In particular, improvar generates values for all the fields
listed in the header, even if your template didn't, allowing you to test your analysis pipeline with
more completely.
Install improvar using:
pip install 'git+https://github.com/TMiguelT/Improvar#egg=improvar'Note that improvar will only work on Python 3.6 and above
improvar installs a command-line utility called improvar. Its usage is as follows:
usage: improvar [-h] [--num-variants NUM_VARIANTS]
[--gt-opts {GenotypeOption.HOM_REF,GenotypeOption.HOM_ALT,GenotypeOption.HET}]
[--include-contig INCLUDE_CONTIG]
[--exclude-contig EXCLUDE_CONTIG]
template_vcf
Generates a fake VCF based on another VCF's header
positional arguments:
template_vcf The VCF to base the generated data off
optional arguments:
-h, --help show this help message and exit
--num-variants NUM_VARIANTS, -n NUM_VARIANTS
Number of variants to print
--gt-opts {GenotypeOption.HOM_REF,GenotypeOption.HOM_ALT,GenotypeOption.HET}
Constraints to apply when generating genotype. Leave
empty to generate entirely random genotypes. Use "het"
to generate only heterozygotes (e.g. 0|1), use "hom-
ref" to generate only homozygous referencegenotpyes
(e.g. 0|0), and use "hom-var" to generate only
homozygous variant genotypes (e.g. 1|1)
--include-contig INCLUDE_CONTIG
Only output contigs whose name matches this regex
pattern
--exclude-contig EXCLUDE_CONTIG
Do not output contigs whose name matches this regex
pattern
improvar prints the generated VCF to stdout, so you can pipe the results of this program to a file
or to other VCF processing tools