How does picard mark duplicates work?

How does picard mark duplicates work?

It takes all clipping into account as well as any gaps or jumps in the alignment. Matches all read pairs using the 5′ coordinates and their orientations. It marks all but the “best” pair as duplicates, where “best” is defined as the read pair having the highest sum of base qualities of bases with Q ≥ 15.

What is an optical duplicate?

A read is called as an optical duplicate if the pair of reads are both on the same tile, and the distance between reads is less than the distance set in Picard’s “Mark Duplicates”.

Why does Picard Mark duplicate?

Duplicate reads can also result from a single amplification cluster, incorrectly detected as multiple clusters by the optical sensor of the sequencing instrument. These duplication artifacts are referred to as optical duplicates.

How do you run a Picard jar?

Quick Start

1. Download Software. The Picard command-line tools are provided as a single executable jar file.
2. Install. Open the downloaded package and place the folder containing the jar file in a convenient directory on your hard drive (or server).
3. Test Installation.
4. Use Picard Tools.

Is Picard part of GATK?

Starting with version 4.0, GATK contains a copy of the Picard toolkit, so all Picard tools are available from within GATK itself. Their documentation is available in the Tool Index section of this website.

When to use MarkDuplicates ( Picard ) in GATK?

MarkDuplicates (Picard) GATK Team. 1 year ago. Updated. Identifies duplicate reads. This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA. Duplicates can arise during sample preparation e.g. library construction using PCR.

When do you use MarkDuplicates ( Picard ) in Bam?

MarkDuplicates (Picard) Identifies duplicate reads. This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA. Duplicates can arise during sample preparation e.g. library construction using PCR.

How to mark all optical duplicates in Picard?

Invoking the TAGGING_POLICY option, you can instruct the program to mark all the duplicates (All), only the optical duplicates (OpticalOnly), or no duplicates (DontTag).

When to remove duplicates, MarkDuplicates does not?

If, however, I add ‘REMOVE_DUPLICATES’=true to the MarkDuplicates command, the singly mapped duplicates are removed but the unmapped mates remain in the resulting file. This is undesirable behavior and these unmapped mates should also be removed. This bug applies to MarkDuplicates and likely MarkDuplicatesWithMateCigar as well.