java -jar GenomeAnalysisTK.jar -T ErrorRatePerCycle -R reference.fasta -I my_sequence_reads.bam -o error_rates.gatkreport.txt
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 |