phe.variant.MPileupVariantCaller module

Date:22 Sep, 2015 Author:Alex Jironkin

class MPileupVariantCaller(cmd_options=None)

Bases: phe.variant.VariantCaller

Implemetation of the Broad institute’s variant caller.

Methods

create_aux_files(ref)	Index reference with faidx from samtools.
get_info([plain])
get_meta()	Get the metadata about this variant caller.
get_version()
make_vcf(*args, **kwargs)
validate()	Check if the command can run.

create_aux_files(ref)

Index reference with faidx from samtools.

Parameters:

ref: str

Path to the reference file.

Returns:

bool:

True if auxiliary files were created, False otherwise.

get_info(plain=False)

get_version()

make_vcf(*args, **kwargs)

name = 'mpileup'

Plain text name of the variant caller.