FreeBayes in RNA-seq

[annaquaglieri16]

Hi,
in a previous thread I noticed that FreeBayes does not to work well with RNA-Seq data. I am in the process of comparing different tools for RNA-Seq variant calling and I was wondering if it is now ok to use it and especially what type of pre-processing it requires (any from the GATK best practices?).

Thanks,

Anna

[annaquaglieri16]

In

bcbio/bcbio-nextgen#389

it was claimed that

@mjafin and others, freebayes should now handle the spliced reads. If this isn't the case please ping me over on the freebayes repo. The only problem I remember was during left alignment of indels. I don't have the commit I'd handy but I believe it has been resolved.

Does it mean that it will handle correctly spliced reads without any pre-processing?

Thanks,

Anna

[xgrau]

May I resurface this issue, in case the OP or the devs have any input on this?

I'm particularly interested in this last question:

Does it mean that it will handle correctly spliced reads without any pre-processing?

Cheers

[for-giobbe]

I am interested as well!

[winni2k]

Me too.

[pjotrp]

freebayes is in maintenance mode. But if anyone wants to work on RNAseq code feel free to reopen this issue.

[winni2k]

Hi @pjotrp. I appreciate that freebayes is in maintenance mode. However I don't think this is an enhancement issue. This issue is merely a request for clarification. The functionality described in this issue may already exist. We would really just like to know if it does.

[winni2k]

freebayes is in maintenance mode. But if anyone wants to work on RNAseq code feel free to reopen this issue.

How would I reopen this issue?

[sanjaynagi]

Id also be keen to know this @winni2k