CLC bio - GATK

[spreeth84]

I have been using CLC bio for over a year and quite happy with the analysis results so far. I also find GATK very useful. It is just painful to export files from one to the other and use both. I know CLC bio has a developer kit for Java developers and GATK is in Java. I am just curious to know if anyone has tried integrating GATK into CLC bio or if it is even possible. (I am not much of a Java developer)

[adaptivegenome]

What exactly do you want to integrate? What do you use CLC bio for and what do you want to do with GATK?

[spreeth84]

Hi , I use CLC Bio for the alignment, coverage calculations and SNP detection. In some cases I use GATK to recalibrate the quality scores before SNP analysis. I find that CLC Bio aligner works well for what we are doing and would like to continue using that for the alignment and the visualization too. But some tools in the GATK like the Base quality score recalibration and realignment around indels would be very useful. I would also like to use the Unified Genotyper to call SNPs. AT this point, I export the sam files from clc bio to use with GATK and sometimes import the resulting sam files back.

[adaptivegenome]

I suppose you could pull the GATK source and integrate it into the CLC Bio SDK. However, GATK gets updated so frequently it is probably not worth trying to integrate it into CLC bio. Just align your reads with CLC Bio, export and do the rest (recalibration, local realignment, etc.) with GATK...