phe.variant_filters.QualFilter module

Filter VCF on GQ parameter.

Date:24 Sep, 2015
Author:Alex Jironkin
class QualFilter(args)[source]

Bases: phe.variant_filters.PHEFilterBase

Filter sites by QUAL score.

Methods

__call__(record) Filter a vcf.model._Record.
decode(filter_id) Decode name of filter.
filter_name() Create filter names by their parameter separated by magic.
get_config() This is used for reconstructing filter.
is_uncallable(record) Filter a vcf.model._Record.
call_concensus  
customize_parser  
is_gap  
is_n  
short_desc  
classmethod customize_parser(parser)[source]

hook to extend argparse parser with custom arguments

name = 'LowSNPQual'
parameter = 'qual_score'
short_desc()[source]

Short description of the filter (included in VCF).