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_meta()	Get the metadata about this variant caller.

get_info
get_version
make_vcf
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 information about this variant caller.

get_version()

Get the version of the underlying command used.

make_vcf(*args, **kwargs)

Create a VCF from BAM file.

Parameters:

ref: str

Path to the reference file.

bam: str

Path to the indexed BAM file for calling _variants.

vcf_file: str

path to the VCF file where data will be written to.

make_aux: bool, optional

True/False create auxilliary files (default: False).

Returns:

bool:

True if variant calling was successful, False otherwise.

name = 'gatk'

Plain text name of the variant caller.

validate()

Check if the command can run.