ReadCounts Read Filtering

The aligned reads covering a specific locus may, for a variety of reasons, not be a reliable observation of the reference or variant alleles at that site. The ReadCounts suite provides a flexible filtering system that can be tailored as needed to ensure reliable allele counts.

The available read-filtering strategies are defined in the file filter.ini in the ReadCounts distribution. New or modified read-filtering strategies can be created, using the same format in a filter.ini file in the current working directory. Named filtering strategies in the current working directory override those with the same name in the ReadCounts distribution.

Read-Filtering Strategies

Basic

Filter out alignments flagged as SECONDARY, DUPLICATE, UNMAPPED, or QCFAIL, and those with a gap or indel at SNV locus. This is the minimal recommended filtering strategy.

ReadCounts:Defaults

Original ReadCounts alignment filtering strategy with default parameters.

ReadCounts:Parameterized

ReadCounts alignment filtering strategy with explicit parameter values.

Explicit:Defaults

Filter in which every filter rule is applied with explicit default parameters. Unmodified, this filtering strategy is equivalent to the Basic filter.

MPileup

Filter reads in a manner similar to samtools/vcftools/bcftools mpileup command-line tool. Filters implement the –ff, -Q, -A, and -x mpileup options.

Read Filters

BasicFilter

Parameters: skip_duplicate=True skip_secondary=True skip_qcfail=True skip_unmapped=True

Optionally filter out alignments flagged as SECONDARY, DUPLICATE, UNMAPPED, or QCFAIL, and those with a gap or indel at SNV locus.

SNVPileupReadFilter

Parameters: minpad=3 minsubstdist=3 maxedits=1 maxsegments=1 minlength=45 maxhits=1 mapq=4

Filter implementing the original ReadCounts filtering strategy. Deprecated.

BaseQualityFilter

Parameters: min_base_quality=None

Minimum required base quality at the specific locus. Default: no minimum base quality.

MappingQualityFilter

Parmeters: min_mapping_quality=None

Minimum required mapping quality at the specific locus. Default: no minimum mapping quality.

ReadLengthFilter

Parameters: min_length=None

Minimum required length for the read. Default: No minimum length.

EditsFilter

Parameters: max_edits=None

Maximum number of edits for the alignment. Includes the substitution observed in reads for the variant allele. References the NM tag. Default: No maximum number of edits.

HitsFilter

Parameters: max_hits=None

Maximum number of alignment placements for the read. References the NH tag. Default: No maximum number of hits.

EditPositionFilter

Parameters: min_edge_dist=None min_subst_dist=None max_other_edits=None

Filter reads based on a) the proximity of the site of interest to the beginning or end of the read, b) the proximity of the nearest edit to the site of interest, or c) total number of edits other than at the site of interest. Default: Keep all reads.

SegementsFilter

Parameters: max_segments=None

Maximum number of segments (separated by gaps) in the read alignment. Default: No maximum number of segments.

OverlapFilter

Pameters: remove=False

When a site of interest is covered by both reads of a read-pair, just one is retained. Default: Retain all reads.

OrphanFilter

Parameters: remove=False

When a paired-end read’s mate is unmapped, do not count the read. Default: Ratain all reads.

UniqueReads

Parameters: remove_dups=False

Ensure exactly duplicate reads are counted exactly once. Default: Do not remove duplicate reads.

Examples

Basic

[Basic]
Description:    (Optionally) Filter out alignments flagged as SECONDARY, DUPLICATE,
		UNMAPPED, or QCFAIL, and those with a gap or indel at
		SNV locus. This is the minimal recommended filtering strategy.
BasicFilter: skip_duplicate=True skip_secondary=True skip_qcfail=True skip_unmapped=True

MPileup

[MPileup]
Description: Filter reads in a manner similar to samtools/vcftools/bcftools
             mpileup command-line tool. Filters implement the --ff, -Q, -A,
	     and -x mpileup options.
BasicFilter:          skip_duplicate=True
                      skip_secondary=True
                      skip_qcfail=True
                      skip_unmapped=True
BaseQualityFilter:    min_base_quality=13
OverlapFilter:        remove=True
OrphanFilter:         remove=True