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.
Any number of BAM files
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
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
These Read Filters are automatically applied to the data by the Engine before processing by ErrorRatePerCycle.
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).
This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.
|--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|
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.
Minimum read mapping quality required to consider a read for calling.
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.