Compute the read error rate per position
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.
Any number of BAM files
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
java -jar GenomeAnalysisTK.jar \
-T ErrorRatePerCycle \
-R reference.fasta \
-I my_sequence_reads.bam \
-o error_rates.gatkreport.txt
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.
This tool applies the following downsampling settings by default.
All tools inherit arguments from the GATK Engine' "CommandLineGATK" argument collection, which can be used to modify various aspects of the tool's function. For example, the -L argument directs the GATK engine to restrict processing to specific genomic intervals; or the -rf argument allows you to apply certain read filters to exclude some of the data from the analysis.
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 |
stdout | 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 | |
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.
Minimum base quality required to consider a base for calling
Integer 0 [ [ -∞ ∞ ] ]
Minimum read mapping quality required to consider a read for calling
Integer 20 [ [ -∞ ∞ ] ]
An output file created by the walker. Will overwrite contents if file exists
PrintStream stdout