cellink.tl.run_vep

cellink.tl.run_vep(config_file='../configs/vep.yaml', input_vcf='variants.vcf', output='variants_vep_annotated.txt', return_annos=True, **kwargs)

Calls the VEP command line tool from within python

Requires VEP to be installed (Tested with VEP v108)

Parameters:

• config_file (_type_) – config file specifying VEP paths as in example/config.yaml

• input_vcf (str) – VCF with variants to annotate. By default “variants.vcf”

• output (str) – File where VEP writes the annotated variants by default “variants_vep_annotated.txt”

• return_annos (bool) – Should the written annotations be loaded into memory.by default False

Returns:

None if return_annos=False else the written annotations loaded into a Pandas Data Frame