Select an output directory. Custom – specify the output directory in the ‘Custom directory’ parameter. Workflow – internal workflow directory. Input file – use its directory.
(none)
out-mode
numeric
Output name
Name of an output BAM/SAM file. If empty, uses the name of the first input file with a .filtered extension.
(none)
out-name
string
Output format
Format of the output assembly file.
bam
out-format
string
Region
Regions to filter (BAM only). Example: chr2, chr2:1000, or chr2:1000-2000. Multiple regions are separated by space.
(none)
region
string
MAPQ threshold
Minimum MAPQ quality score.
0
mapq
numeric
Accept flag
Output alignments matching selected flags. Leave empty to skip this filter.
(none)
accept-flag
string
Skip flag
Skip alignments matching selected flags. Leave empty to skip this filter.