Wish: Support ensemble for paired analyses

bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

https://bcbio-nextgen.readthedocs.io

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Wish: Support ensemble for paired analyses #67

Closed lbeltrame closed 7 years ago

lbeltrame commented 11 years ago

This is an approach that has been used in a few recent papers, and I think would be a worthwhile addition to the pipeline. There are some points to make:

[ ] Ensure there are n > 1 methods available (depends on #65, #66 )
[ ] Check whether bcbio-variation can work with these OOTB
[ ] See if the pipeline can handle filtering for these: Somatic Sniper has a SS (somatic score), I need to check for VarScan, and MuTect has REJECT/PASS in the VCF FILTER field.

Would this make sense ti implement?

chapmanb commented 11 years ago

The Cake pipeline is worth exploring.

http://cakesomatic.sourceforge.net/

This would require including Cake and associated tools in CloudBioLinux for installation and then wrapping Cake as a variant caller in bcbio-nextgen,

lbeltrame commented 11 years ago

I looked through the Cake documentation and it would still require quite a lot of work to get it right. Plus, as far as I can understand, part of the pipeline depends on Ensembl genomes (and that means that people using UCSC would be left out in the cold).

lpantano commented 7 years ago

I am closing this because it seems an old issue. Come back if you find other issues or want to continue with this one.

cheers