Hi,

I'm working with dna-seq data from pancreatic cancer patients, and is trying to create an ensemble of somatic variant calls from different variant callers. The idea is to use bcbio.variation for this purpose. However, I'm not sure how to best deal with biological replicates. As I see it, I can either:

1. Merge the aligned files from the biological replicates and call variants on the merged files.
2. Call variants on the aligned files and combine the variant calling outputs. (fx. when creatin the ensemble)

I seem to be unable to find litterature concerning this. So I wonder how best to deal with biological replicates when calling somatic variants.

Best regards