Collection of variant callers based on BGM AB (allele balance) and bayesian callers.
This package includes a hraness to run BGM Rare Variant Callers. Currently implemented callers are:
Allele Balance Callers:
- De-Novo
- Homozygous Recessive
- Compound Heterozygous
Bayesian Callers:
- De-Novo
The easiest way to run callers is to use variant_caller.py module.
usage: variant_caller.py [-h] -i VCF -f FAMILY [--results RESULTS]
[--dnlib DNLIB]
Run BGM variant callers
optional arguments:
-h, --help show this help message and exit
-i VCF, --input VCF, --vcf VCF
Input VCF file, required. Use jointly called VCF for
better results
-f FAMILY, --family FAMILY
Family (fam) file, required
--results RESULTS Results directory, only used for running Bayesian
callers
--dnlib DNLIB Path to De-Novo library. If specified, then Bayesian
De-Novo Caller is used, otherwise Allele Balance
Caller
Additional information on customized use of Bayesian De-Novo caller is in
package denovo2. In the same file is the instruction to build a custom
De-Novo library. A prebuild library from prior BGM cases is available
for download.
To include this variant caller in the pipeline see variant_caller.py and callers/harness.py modules