Category

Genome Variant Analysis


Usage

java -jar GenomeAnalysisTK.jar -T PrintReads -R reference.fasta -I input.bam -o output.file -rf ReassignMappingQuality -DMQ 35


Manual

Argument name(s)Default valueSummary
Optional Parameters
--default_mapping_quality
 -DMQ
60Default read mapping quality to assign to all reads


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