# ErrorRatePerCycle

Compute the read error rate per position

## Overview

This tool computes the read error rate per position in sequence reads. It does this in the original 5'->3' orientation that the read had coming off the machine. It then emits a GATKReport containing readgroup, cycle, mismatches, counts, qual, and error rate for each read group in the input BAMs.

### Input

Any number of BAM files

### Output

A GATKReport containing readgroup, cycle, mismatches, counts, qual, and error rate. For example, running this tool on the NA12878 data sets yields the following table:

      ##:GATKReport.v0.2 ErrorRatePerCycle : The error rate per sequenced position in the reads
readgroup  cycle  mismatches  counts  qual  errorrate
20FUK.1        0          80   23368    25   3.47e-03
20FUK.1        1          40   23433    28   1.75e-03
20FUK.1        2          36   23453    28   1.58e-03
20FUK.1        3          26   23476    29   1.15e-03
20FUK.1        4          32   23495    29   1.40e-03
up to 101 cycles
20FUK.2        0          77   20886    24   3.73e-03
20FUK.2        1          28   20920    29   1.39e-03
20FUK.2        2          24   20931    29   1.19e-03
20FUK.2        3          30   20940    28   1.48e-03
20FUK.2        4          25   20948    29   1.24e-03
up to 101 cycles
20FUK.3        0          78   22038    24   3.58e-03
20FUK.3        1          40   22091    27   1.86e-03
20FUK.3        2          23   22108    30   1.09e-03
20FUK.3        3          36   22126    28   1.67e-03


### Example

    java
-jar GenomeAnalysisTK.jar
-T ErrorRatePerCycle
-R human_g1k_v37.fasta
-o error_rates.gatkreport.txt


### Caveat

Note that when it is run on paired-end sequence data, this tool only uses the first read in a pair.

These Read Filters are automatically applied to the data by the Engine before processing by ErrorRatePerCycle.

### Downsampling settings

This tool applies the following downsampling settings by default.

• Mode: BY_SAMPLE
• To coverage: 1,000

## Command-line Arguments

### Inherited arguments

The arguments described in the entries below can be supplied to this tool to modify its behavior. For example, the -L argument directs the GATK engine restricts processing to specific genomic intervals (this is an Engine capability and is therefore available to all GATK walkers).

### ErrorRatePerCycle specific arguments

This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.

Argument name(s) Default value Summary
Optional Outputs
--out
-o
NA An output file created by the walker. Will overwrite contents if file exists
Optional Parameters
--min_base_quality_score
-mbq
0 Minimum base quality required to consider a base for calling
--min_mapping_quality_score
-mmq
20 Minimum read mapping quality required to consider a read for calling

### Argument details

Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.

### --min_base_quality_score / -mbq

Minimum base quality required to consider a base for calling

Integer  [ [ -∞  ∞ ] ]

### --min_mapping_quality_score / -mmq

Integer  [ [ -∞  ∞ ] ]

### --out / -o

An output file created by the walker. Will overwrite contents if file exists

PrintStream