[skruglyak]

ok, thanks for the info.

Will isaac2 perform on whole exome data as good as on whole genome data?

Isaac2 will work well on exome. The multiplicative speed factor increase over other aligners will not be as high due to the fixed costs (reading in the index, demultiplexing) and the relatively small number of reads to align.

In our experience, the variant calls from a whole genome assay are better than the variant calls from an exome assay, but that is due to factors such as coverage uniformity and not the aligner.

[sklages]

OK .. index creation is running for hg19 ... I'll report back tomorrow.

Btw, .. is starling2 (ivc) still the "variant caller to work with"? Or do you recommend other variant callers for isaac2-aligned data? I am just asking because it seems that there is not much development on github (sequencing) ...

[skruglyak]

OK .. index creation is running for hg19 ... I'll report back tomorrow.

Btw, .. is starling2 (ivc) still the "variant caller to work with"? Or do you recommend other variant callers for isaac2-aligned data? I am just asking because it seems that there is not much development on github (sequencing) ...

Any of the variant callers should work with Isaac BAMs. We have continued Starling (a.k.a Isaac variant caller) development, but it will take a bit more time for us to get the latest version on GitHub.

[skruglyak]

That's funny though .. under normal circumstances I'd remove this folder as it occupies quite a lot of disk space ..

I have asked Come to address the issues that you are seeing and to also start a new thread (or Google group) dedicated to Isaac support.

Thanks,

Semyon

[GenoMax]

I have asked Come to address the issues that you are seeing and to also start a new thread (or Google group) dedicated to Isaac support.

Thanks,

Semyon

Posts related to isaac2 genome index creation have been moved into a new thread: http://seqanswers.com/forums/showthread.php?t=61539 to keep this thread focused on open source software from Illumina.

[skruglyak]

Several more tools have now been added to GitHub.com/Illumina.

Canvas: a tool for calling copy number variants that can be used in either germline data or tumor / normal samples.

Hap.py: a tool for comparing VCF files by haplotype. This means that variants with multiple representations will still be matched correctly.

pyFlow: a python module to manage tasks in the context of a task dependency graph. We previously used Make in this context, but developers have found pyFlow to be a much better experience.

[ctsa]

Just the kind of information I was asking for. Thanks!

Can minimal/optimal hardware specs be noted on the respective pages so people can make an informed decision on whether they should try using that package. e.g. isaac (and possibly isaac2, going to try it soon) needs reasonably potent hardware.

Thanks for the suggestion. we've added hardware guidelines to the latest manta update here:

https://github.com/Illumina/manta#runtime-hardware-requirements

Hope this helps!

[pkrusche]

Hardware and system requirements for hap.py have been added here:

https://github.com/Illumina/hap.py#hardware-and-os-requirements

Peter

[skruglyak]

We recently released Manta on GitHub under GPLv3.
In case people would like to take a closer look at how Manta works:

Preprint for our open-source Manta SV & indel caller (from DREAM SMC)
now on Biorxiv:http://biorxiv.org/content/early/2015/08/10/024232
Source: https://github.com/Illumina/manta

[skruglyak]

Additional open source tools

Hi everyone,

we have just released Pisces somatic variant caller (manuscript in preparation) to our GitHub site. This method is used to call somatic SNVs, MNVs, and small indels in MSR and several BaseSpace applications. The analysis applies to targeted sequencing of tumor samples.

Other recent releases to the site include MarViN (used to refine genotypes in WGS data) and agg (used to rapidly merge gVCF files).

Thanks and happy holidays,

Semyon

[dmb107]

Error with Canvas

Hi, I am trying to use Canvas for Germline WGS, and I am running into a fatal error. Could someone on this thread help me?

ERROR: Canvas workflow error: Illumina.SecondaryAnalysis.JobFailedException: mono returned error code -1

[skruglyak]

Hi, I am trying to use Canvas for Germline WGS, and I am running into a fatal error. Could someone on this thread help me?

ERROR: Canvas workflow error: Illumina.SecondaryAnalysis.JobFailedException: mono returned error code -1

Yes, I have alerted the developers. They will likely ask you for additional details and the data set that you are using.

[dmb107]

Thank you for your fast response!

[sivakhno]

Thank you for your fast response!

Could you perhaps share log files for the run, they should be in:
output\CanvasError.txt
output\CanvasLog.txt
output\Logging\*

One way to share these is to create a new issue on the Canvas GitHub page https://github.com/Illumina/canvas/issues/new and attach aforementioned files