ErrorRatePerCycle

Computes the read error rate per position in read (in the original 5'->3' orientation that the read had coming off the machine) Emits a GATKReport containing readgroup, cycle, mismatches, counts, qual, and error rate for each read group in the input BAMs FOR ONLY THE FIRST OF PAIR READS.

Category Diagnostics and Quality Control Tools

Traversal LocusWalker

PartitionBy LOCUS

Overview

Input

Any number of BAM files

Output

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

      ##: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

Examples

    java
      -jar GenomeAnalysisTK.jar
      -T ErrorRatePerCycle
      -I bundle/current/b37/NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam
      -R bundle/current/b37/human_g1k_v37.fasta
      -o example.gatkreport.txt

Additional Information

Read filters

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

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).

CommandLineGATK

ErrorRatePerCycle specific arguments

This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.

Name	Type	Default value	Summary
Optional
--min_base_quality_score	Integer	0	Minimum base quality required to consider a base for calling
--min_mapping_quality_score	Integer	20	Minimum read mapping quality required to consider a read for calling
--out	PrintStream	stdout	An output file created by the walker. Will overwrite contents if file exists

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 ( Integer with default value 0 )

Minimum base quality required to consider a base for calling.

--min_mapping_quality_score / -mmq ( Integer with default value 20 )

Minimum read mapping quality required to consider a read for calling.

--out / -o ( PrintStream with default value stdout )

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

GATK version 2.5-2-gdb4546e built at 2013/05/01 09:32:36.