phe.variant_filters.MQ0Filter module

Filter VCF on MQ filter.

Date:24 Sep, 2015 Author:Alex Jironkin

class MQ0Filter(args)

Bases: phe.variant_filters.PHEFilterBase

Filter sites by MQ0 (Total Mapping Quality Zero Reads) to DP ratio.

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)

hook to extend argparse parser with custom arguments

name = 'MinMQ0'

parameter = 'mq0_ratio'

short_desc()

Short description of the filter (included in VCF).