GATK - RealignerTargetCreator ? need to run for all samples in the same experiment ?

[swNGS]

Hi,

Lets say I have 20 bams derived form the same targetted sequencing experiment, and I want to push them through the recommended GATK pipleine.

For the RealignerTargetCreator part of realigning around sites of common indels, should I be running it per sample, or can I run it once against one sample and then use the list filethat it generates against all the other bams from the same experiment, on the basis that since the same regions are being sequenced per sample, the same recurrent indel sites will crop up in each sample.

... or have I minunderstood what the intervals.list file that RealignerTargetCreator defines?

Thanks

[Zaag]

Depends a bit on your coverage. I would do both steps on all bams together unless you have really high coverage (i.e. >100 average).

[swNGS]

My bams are derived from small targeted resequencings experiments, but coverage can be high (several thousand)
So I make it that I can merge bams (each identified with its own read group) then run all the GATK indel realignment steps on the merged bam.

Can I run all of the GATK steps on one merged bam also?

Thanks

[swNGS]

and the answer is that I had assumed correctly that RealignerTargetCretor needs only running once a described here:
http://gatkforums.broadinstitute.org...-around-indels
using -knownsOnly mode, which I assume only looks for indels in the reference files you supply.

I guess that if I dont specify -knownsOnly then it must look for novel indels, which might be a good thing, I'lll have to investigate the overhead that creates first though.

[Zaag]

If you have that high coverage, I would process them one by one for the realignment; all together for the creation of the recalalibration table and one by one again for the second step of the recalibration.

You can give multipe bams as input to the GATK so no need to merge the files beforehand.
Use the -L option with your target bed file to speed up things.

I would recommend looking for novel indels also.