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Old 06-26-2014, 08:04 PM   #1
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Join Date: Jul 2012
Posts: 34
Default some basic questions about duplicate removal ?

Hi all,

I am using the GATK pipeline for pre processing bam files after alignment with bwa mem. The original bam files after alignment shows I have (samtools flagstat command) - 173,460,757 reads (this is deep sequening exome data captured with agilent sure select 50 mb).

But after removing duplicates with Picard, I am left with 14,651,238 reads !! Thats like mere 20X coverage.

1. I would like to know whether this is normal in exome seq to find such huge amount duplicates? And some of the threads on other forums say its not wise to remove duplicates from deep sequencing data. Can anyone provide me some suggestions on this, like how you guys proceed in such scenario ?

2. And what is the difference between marking duplicates and removing duplicates ? I know marking adds a tag instead of completely removing the read. But, if the duplicate marked reads are not used in any of the downstream steps (like SNP calling) why is it suggested to simply marking it instead of removing it?

3. And while calculating coverage do we have to consider duplicate reads as well (original bam) or the final bam file with dups removed ?

Thank you.
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