Hi,

I would like to ask if any of you know the callers of the pipelines that are stated on ICGC such as broad, embl and sanger? I checked the metadata however the website which directed me required id/password accession. These are pipelines that were used for calling mutations which produced VCF files.

Thank you

Best,  
Tunc
Can you put the link you have been looking into? Usually the broad mutation caller is GATK toolkit and Mutect. Often VarScan2 is also used widely. But am assuming that this one you are looking into are the ICGC -TCGA project which is run by multiple sites in the world. I not sure if the publication is out yet. So [it shows only][1] the status of the calls made at all different contributing sites that are a part of this challenge so sequence WGS for large PAN-Cancer panel.

You can take a look at this [link][2] which has a somatic workflow for SNVs . This is of Sanger

I am not sure for the embl but Delly is one which is widely used but that is for SVs and not SNVs. I guess you have to do a bit more digging.

As I said you can find the below links for the different workflows that are being used by 3 major workflow managers , and I believe this is being circulated across different centers where samples are being analyzed.

 - [The DKFZ/EMBL PanCancer Variant Calling Workflow][3]
 - [DKFZ Dockered Workflows][4]
 - [BroadWrapperWorkflow][5]

I think [this link][6] has most of the necessary information you are looking for.

[1]: http://pancancer.info/variant_calling.html
[2]: https://github.com/ICGC-TCGA-PanCancer/SeqWare-CGP-SomaticCore
[3]: https://github.com/ICGC-TCGA-PanCancer/DEWrapperWorkflow
[4]: https://github.com/ICGC-TCGA-PanCancer/dkfz_dockered_workflows
[5]: https://github.com/ICGC-TCGA-PanCancer/BroadWrapperWorkflow
[6]: https://github.com/ICGC-TCGA-PanCancer?page=3