Question: GATK recalibration, duplicates & realignment
gravatar for alons
4.5 years ago by
alons270 wrote:

Hi all, I'm working on a variant calling pipeline based on the following link:

Now, in the "Improvement" section, which mainly uses GATK, it says that I should realign the bam file and then recalibrate and mark the duplicates. What is unclear to me is which bam file is used as input for each step. For example, is the realigned bam file the input of the recalibration step?
I should note that I'm using a single bam file, 1 library.

Thank you, Alon

bam ngs alignment realignment gatk • 2.3k views
ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by alons270
gravatar for Sean Davis
4.5 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

You are correct in your reading.  The steps described are run serially with the output BAM being the input BAM to the next step.

ADD COMMENTlink written 4.5 years ago by Sean Davis25k

Thank you!.
A follow up question, though: in the same section they recommend another realignment, after the improvement steps (initial realignment, recalibration and marking of duplicates).
Is it really necessary if I have only one bam (no merging of several bam files) ? 

ADD REPLYlink written 4.5 years ago by alons270
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