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=== Filtering ===
=== Filtering ===
-b [int] ''exclude bases with quality less than [int]''
-b [int] ''exclude bases with quality less than [int]''
-M [int] ''exclude reads with map quality less than [int]''
-M [int] ''exclude reads with map quality less than [int]''
-F [int] ''set custom BAM flags filter (not implemented at the moment)''
-f [float] ''drop markers with minor allele frequency smaller than [float]''
-F [int] ''set custom BAM flags filter (not implemented at the moment)''
=== Other Options ===
=== Other Options ===
