spikely - spike pathogenic alleles into VCF files.

Synopsis:

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spikely help

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spikely cohort --help

Run cohort spiking mode with parameters defined in a config file.

spikely cohort --config_file spikely.yaml --disease_vcf clinvar.vcf.gz \
    --sample_vcf case_control.vcf.gz

Run trio spiking mode with parameters on the command line.

spikely trio --ped family.ped --inheritance recessive --maf_key MAF \
    disease_alleles.vcf.gz

Description:

This script will consume a VCF file of causal variants and produce a VCF file with those variants 'spiked' into the genotypes of a set of individuals defined by various genetic and population parameters. The script has several modes of operation corresponding to various NGS genetic analysis designs (i.e. trio, pedigree, cohort etc.). It understands genetic concepts such as inheritance, penetrance and population attributable risk and allele population frequency and allows those parameters to be specified in a configuration file. Note that currently only cohort and trio spiking is implimented.

Functions:

help
cohort
trio

# For future developement
duo
quartet1
quartet2
pedigree