phe.variant.MPileupVariantCaller module¶
Date: | 22 Sep, 2015 |
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Author: | Alex Jironkin |
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class
MPileupVariantCaller
(cmd_options=None)[source]¶ Bases:
phe.variant.VariantCaller
Implemetation of the Broad institute’s variant caller.
Methods
create_aux_files
(ref)Index reference with faidx from samtools. get_meta
()Get the metadata about this variant caller. validate
()Check if the command can run. get_info get_version make_vcf -
create_aux_files
(ref)[source]¶ Index reference with faidx from samtools.
Parameters: - ref: str
Path to the reference file.
Returns: - bool:
True if auxiliary files were created, False otherwise.
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make_vcf
(*args, **kwargs)[source]¶ 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.
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name
= 'mpileup'¶ Plain text name of the variant caller.
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