Category

Genome Variant Analysis


Usage

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


Manual

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


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