Ion Torrent and Whole Exome Sequence

[alexdem]

Hi all,

I am a new user of an Ion Torrent and we are working on Whole Exome Sequencing (WES). From what I've read so far, GATK is the golden standard for such analysis when it comes to Illumina data BUT that does not apply so much to Ion Torrent data.
Does anyone have experience on WES with Ion Torrent and can help me by proposing software to use for my pipeline, or alterations on the GATK best practice?

Thank you in advance for your time

[RemitoAmigo]

Far from being a master in the field...Have you had a look at Ion Reporter?

[alexdem]

Well actually I have, but I am trying to find something open-source and not specifically from the producer (LifeTech).

[NextGenSeq]

You can generate FastQ files on the Ion Torrent. I would just use GATK.

The Broad has published ChIP-Seq on the PGM and they must have used GATK.

[Zaag]

GATK does not align reads so what do you use for this?

https://github.com/iontorrent/TS

Is open source TorrentSuite, contains a aligner and variant caller.

[snetmcom]

The Torrent Suite has specific settings for exome analysis already. I'm not sure why you would want to use other tools.

[alexdem]

Thank you for the suggestion. I will definitely try TorrentSuite!

Do you know if it the same software as the one running on Ion Proton?

[GenoMax]

AFAIK: Torrent suite download available on github does not include Ion reporter (which is not free software). If you have access to an ion machine then there is likely to be a copy there that you can use for the variant calling/coverage analysis.

[alexdem]

Thank you, I'll look into it.

[BrianJames]

Thank you for the suggestion. I will definitely try TorrentSuite!

Do you know if it the same software as the one running on Ion Proton?

Yes, TS is the same as what is running your Ion Proton.
Brian

[Jeremy]

Ion reporter uses gatk doesn't it? Very little of the Ion torrent software is made by lifetech, most of it is just the freely available software with the default settings tweaked for torrent data.

[BrianJames]

I'm not sure what Ion Reporter uses, but the torrent server uses TMAP to align reads.

[Jeremy]

I'm not sure what Ion Reporter uses, but the torrent server uses TMAP to align reads.

Yeah, but TMAP is basically just a wrapper for BWA with the defualt being BWA fastmap.

[snetmcom]

TMAP is mostly BWA but it runs it in an iterative process. It also takes their flow bam files. I almost always see more data aligning with TMAP.

Ion Reporter and the server uses the same alignment and variant calling tools. The reporter software adds database annotation to the variants called with FreeBayes.

[mbzmg1]

We have had success using GSNAP to map Ion Torrent reads -especially for RNAseq with splicing. Tophat2/Bowtie2 do not deal well with Ion Torrent data.