Filter out reads with low mapping qualities
This filter is intended to ensure that only reads that are likely to be mapped in the right place, and therefore to be informative, will be used in analysis.
java -jar GenomeAnalysisTk.jar \ -T HaplotypeCaller \ -R reference.fasta \ -I input.bam \ -o output.vcf \ -rf MappingQuality \ -mmq 15
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|
|10||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 read mapping quality required to consider a read for calling
int 10 [ [ -∞ ∞ ] ]
GATK version 3.7-0-gcfedb67 built at 2017/02/09 12:35:06.