CallOverlappingConsensusBases

Overview

Group: SAM/BAM

Consensus calls overlapping bases in read pairs.

Inputs and Outputs

In order to correctly correct reads by template, the input BAM must be either queryname sorted or query grouped. The sort can be done in streaming fashion with:

samtools sort -n -u in.bam | fgbio CallOverlappingConsensusBases -i /dev/stdin ...

The output sort order may be specified with --sort-order. If not given, then the output will be in the same order as input.

The reference FASTA must be given so that any existing NM, UQ and MD tags can be repaired.

Correction

Only mapped read pairs with overlapping bases will be eligible for correction.

Each read base from the read and its mate that map to same position in the reference will be used to create a consensus base as follows:

1. If the base agree, then the chosen agreement strategy (--agreement-strategy) will be used.
2. If the base disagree, then the chosen disagreement strategy (--disagreement-strategy) will be used.

The agreement strategies are as follows:

• Consensus: Call the consensus base and return a new base quality that is the sum of the two base qualities.
• MaxQual: Call the consensus base and return a new base quality that is the maximum of the two base qualities.
• PassThrough: Leave the bases and base qualities unchanged.

In the context of disagreement strategies, masking a base will make the base an “N” with base quality phred-value “2”. The disagreement strategies are as follows:

• MaskBoth: Mask both bases.
• MaskLowerQual: Mask the base with the lowest base quality, with the other base unchanged. If the base qualities are the same, mask both bases.
• Consensus: Consensus call the base. If the base qualities are the same, mask both bases. Otherwise, call the base with the highest base quality and return a new base quality that is the difference between the highest and lowest base quality.

Arguments

Name	Flag	Type	Description	Required?	Max # of Values	Default Value(s)
input	i	PathToBam	Input SAM or BAM file of aligned reads.	Required	1
output	o	PathToBam	Output SAM or BAM file.	Required	1
metrics	m	FilePath	Output metrics file.	Required	1
ref	r	PathToFasta	Reference sequence fasta file.	Required	1
threads		Int	The number of threads to use while consensus calling.	Optional	1	1
sort-order	S	SamOrder	The sort order of the output. If not given, output will be in the same order as input if the input.	Optional	1
agreement-strategy		AgreementStrategy	The strategy to consensus call when both bases agree. See the usage for more details	Optional	1	Consensus
disagreement-strategy		DisagreementStrategy	The strategy to consensus call when both bases disagree. See the usage for more details	Optional	1	Consensus