I wonder how well GATK works with Ion Torrent data. Is there any recommended practice to handle Ion Torrent data, especially SNP and indel calling, with GATK?
This is a very good question. We do have reasonably extensive experience with GATK on Ion Torrent (PGM and Proton) and we've been meaning to put together a best practices doc for Ion Torrent. My two cents: we can do reasonably well for SNP but indels are I think impossible today given the homopolymer error mode of that sequencers. I have yet to see any compelling evidence that indels can be done effectively using any approach -- not just GATK -- including the example results on the Ion Community itself.
Thanks for your prompt response, Mark. I understand that the variant caller developed by Ion Torrent uses a modified version of GATK, which includes a flow space modelling function to tackle the homopolymer issue. Do you have any experience with that? If I want to call INDELs with on Ion data with GATK now, would you recommend using the current INDEL pipeline -- indel realignment, UnifiedGenytyper with glm set to DINDEL and hard filtering?
All good questions -- things we'll address on the best practices entry.
Is there more known about using GATK for variant calling SNPS and Indels?
Niels, if you mean to ask about calling variants on Ion Torrent data, we have not yet had the time to produce that documentation.
Update to this thread: we are no longer working with Ion Torrent at all and will not produce best practices for dealing with this data type.
So no way we can use Ion Torrent data with GATK for variant calling ?
Sure, you can use it on your own, but we won't be able to help you if you have issues.
Is it difficult to make a pipeline for Ion torrent data. I don't feel good when I heard GATK does not give support for best call practice
I think the issue is that the sequencer has some funny indel error modes. GATK is not designed to handle those. But, you are free to use the Best Practices workflow and try. We just cannot guarantee the best results, especially around indels. If you do a search for Ion Torrent, you may find some helpful threads.