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Samtools markdup (version 1.15.1+galaxy2)

Alignment:

Remove duplicate reads:

Mark supplementary reads of duplicates as duplicates:

Clear previous duplicate settings and tags.:

Expected maximum read length of INT bases. (default 300, min=0):

Optical distance (if set, marks with dt tag, min=1):

Duplicate decision method for paired reads.:

Include quality check failed reads.:

Output Options

Output Options 0

Mark duplicate alignments from a coordinate sorted file that has been run through fixmate with the -m option. This program relies on the MC and ms tags that fixmate provides.

Note: The Galaxy tool sorts the data automatically if the input is SAM or query name sorted. The output is BAM (which is query name sorted again if the input is).

The optional basic statistics output of samtools markdup can be visualized with MultiQC.