Filter Duplicate reads

[AP]

Hi Could you please let me know on what basis you would calculate the number that appears when I have "Filter Duplicate Reads" box checked?

Are ONLY PCR Optical duplicates ( with SAM format flag - 1024 ) be filtered out OR any additional criteria besides PCR Optical duplicates?

Please let me know,

Aparna

[James Robinson]

This option relies on the SAM format flag,  no other criteria.

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[Aparna]

Hi Jim,

This data is Illumina , paired end data aligned with  bwa-mem ( with -M flag to mark secondary alignments) and pcr duplicates marked (using Picard MarkDuplicates).This is not RNAseq data.

I'm using bwa 0.7.10 and samtools,1.1 and IGV, 2.3.98.

What do you think the criteria is?

Also, I noticed that IGV has " Filter Duplicate Reads" instead " Filter Optical Duplicates" which would implicate 1024 Sam flag.

Pl let me know,

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[James Robinson]

Hi, the criteria is simple,  if Picard, or any other tool,  marks a read as a duplicate  (with flag 1024) its filtered.   The sam spec indicates this flag is for a "PCR or optical duplicate",  but IGV doesn't care if the flag is set its filtered.