count duplicates in bam files

[Flo89]

Hi,

I would like to count duplicates in bam files. I am comparing two mapping tools and looking at the total counts. Typically, it should be the same
value. My assumption is that BWA mem counts duplicates.

What I did:

1) convert sam -> bam file
2) sort bam file
3) use the Picard tool MarkDuplicates.jar
4) use the BuildBamIndex.jar

Mapped Reads (CLC) 6,876,285
Mapped Reads (BWA) 6,375,889
Unmapped Reads (CLC) 231,927
Unmapped Reads (BWA) 7,367,30
Total count (CLC) 7,108,212
Total count (BWA) 7,112,619

What would be the next step ? I ve tried to use the .bai files ... but do they have information about the number of duplicates ?

Do you have any suggestions ?

Best,
Flo

[GenoMax]

If you are just looking to get the total number of duplicates you could run Qualimap on your bam files. You will get all sorts of additional info as well.

This thread has some other suggestions: http://seqanswers.com/forums/showthread.php?t=23493

[blancha]

Doesn't the metrics file produced by MarkDuplicates.jar already contain the information the duplicate counts?

[GenoMax]

Doh! A file name is required for Metrics file so @Flo89 must have provided it when running MarkDuplicates.

[Flo89]

Hi guys,

Thank you very much. I am not familiar with this mapping stuff. So, I guess it was an easy question for you guys.

Best,
Flo