## Mark duplicates in BAM

### Description

Mark duplicates in the flag field in BAM.

### Parameters

None

### Details

Examines aligned records in the supplied BAM file to locate duplicate molecules. All records are then written to the output file with the duplicate records flagged. This tool is based on the Picard tool MarkDuplicates.

### Output

Output is a BAM file with the duplicate flag set, and a tsv file containing the statistics.

### References

This tool is based on the Picard package.