Can IonProton sequencing data be processed using BWA + FreeBayes or CLC?

Question

[William]

Iontorrent data used to have big homopolymer issues, the sequencing machine did output some Iontorrent specific quality information that only Iontorrent specific aligners and variant calling software could use.

The homopolymer issue seems to have been improved with the IonProton machine, but it's still an issue.

Do I still need IonProton specific software for alignment and variant calling? (which I do not have access to).

Or can I use for example BWA+Freebayes for alignment and variant calling of IonProton fastq data? Or maybe CLC?

[sridhar56]

I just checked CLC Genomics Workbench and see that you can import Ion torrent data. It should be able to handle the data and I would assume you would have to filter out the homopolymers in your data.

I would assume you can also use the BWA, Freebayes to work with Ion torrent data, it should not be a problem.

[Titus]

Hi I use bwa on Ion torrent data and i have results ( in number of reads aligned ) quit similar to Iontorrent specific aligners. The problem is INDEL and homopolymer but it's not perfect with Iontorrent specific aligners.

Best