phe.variant.GATKVariantCaller module

Date:22 Sep, 2015 Author:Alex Jironkin

class GATKVariantCaller(cmd_options=None)

Bases: phe.variant.VariantCaller

Implemetation of the Broad institute’s variant caller.

Methods

create_aux_files(ref)	Create auxiliary files needed for this variant.
get_info([plain])
get_meta()	Get the metadata about this variant caller.
get_version()
make_vcf(*args, **kwargs)
validate()

create_aux_files(ref)

Create auxiliary files needed for this variant.

Tools needed: samtools and picard tools. Picard tools is a Java library that can be defined using environment variable: PICARD_JAR specifying path to picard.jar or PICARD_TOOLS_PATH specifying path to the directory where separate jars are (older version before jars were merged into a single picard.jar).

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 = 'gatk'

Plain text name of the variant caller.

validate()