freebayes on nanopore reads

Question

[Nodilan]

Good morning ,

I have my reads generated using nanopore technology , I already know that there is Medaka, Nanopolish and Clair ( correct if I'm wrong please) but can I use freebayes to detect variants ???

many thanks !!

[GenoMax]

Use one of the workflows at Epi2ME if it fits your user case: https://labs.epi2me.io/wfindex/

[Nodilan]

thank you but besides this , can I use freebayes ?

[GenoMax]

While you can use any program keep in mind its originally intended application. If a program uses assumptions that don't fit the data then you could end up with incorrect results. Have you checked the overview section for freebayes: https://github.com/freebayes/freebayes

Answer 1

[colindaven]

Generally freebayes is a good, robust tool for SNP calling. It requires a lot of downstream filtering by QUAL etc to get good SNP sets though. That is, it focuses on sensitivity, not specificity, so outputs many potential variants.

If you have older reads - eg ONT 9.4.1 - then you will need to do far more quality filtering than the newer Kit14 ONT 10.4.1 datasets.

I would look at longshot as well as it is easy and fast and can output phased SNPs. It is also designed for Nanopore.

[Nodilan]

thank you Sir,

when you say "then you will need to do far more quality filtering than the newer Kit14 ONT 10.4.1 datasets" does it mean that I have to filter my vcf file based on QUAL column ??

what do you recommand as tool in order to visualize if I have a good variant quality or not ? in other words how would I know which quality value I have to setup ?

thanks !! :)