ErrorRateByReadPosition

Overview

Group: SAM/BAM

Calculates the error rate by read position on coordinate sorted mapped BAMs. The output file contains a row per read (first of pair, second of pair and unpaired), per position in read, with the total number of bases observed, the number of errors observed, the overall error rate, and the rate of each kind of substitution error.

Substitution types are collapsed based on the reference or expected base, with only six substitution types being reported: A>C, A>G, A>T, C>A, C>G and C>T. For example, T>G is grouped in with A>C.

Analysis can be restricted to a set of intervals via the --intervals option. Genomic positions can be excluded from analysis by supplying a set of variants (either known variants in the sample or a catalog of known variants such as dbSNP). For data believed to have low error rates it is recommended to use both the --intervals and --variants options to restrict analysis to only regions expected to be homozygous reference in the data.

The following are reads / bases are excluded from the analysis:

• Unmapped reads
• Reads marked as failing vendor quality
• Reads marked as duplicates (unless --include-duplicates is specified)
• Secondary and supplemental records
• Soft-clipped bases in records
• Reads with MAPQ < --min-mapping-quality (default: 20)
• Bases with base quality < --min-base-quality (default: 0)
• Bases where either the read base or the reference base is non-ACGT

An output text file is generated with the extension .error_rate_by_read_position.txt

If R’s Rscript utility is on the path and ggplot2 is installed in the R distribution then a PDF of error rate plots will also be generated with extension .error_rate_by_read_position.pdf.

Arguments

Name	Flag	Type	Description	Required?	Max # of Values	Default Value(s)
input	i	PathToBam	Input BAM file.	Required	1
output	o	PathPrefix	Output metrics prefix. If not given, will use the input BAM basename.	Optional	1
ref	r	PathToFasta	Reference sequence fasta file.	Required	1
variants	v	PathToVcf	Optional file of variant sites to ignore.	Optional	1
intervals	l	PathToIntervals	Optional list of intervals to restrict analysis to.	Optional	1
include-duplicates	d	Boolean	Include duplicate reads, otherwise ignore.	Optional	1	false
min-mapping-quality	m	Int	The minimum mapping quality for a read to be included.	Optional	1	20
min-base-quality	q	Int	The minimum base quality for a base to be included.	Optional	1	0
collapse		Boolean	Collapse substitution types based on the reference or expected base, with only six substitution types being reported: A>C, A>G, A>T, C>A, C>G and C>T.For example, T>G is grouped in with A>C. Otherwise, all possible substitution types will be reported.	Optional	1	true