Minimal size and multiple datasets

[Davide Cittaro]

I'm trying to use delly on a large number of low coverage samples and I get this error:

Sample has not enough data to estimate library parameters! File: …

I now filtered files smaller than 500kb, but I'm curious: which is the smallest dataset size allowed for a delly run?

Given that the samples available for the analysis may influence it, is it expected to have some difference for the following approaches?

- multisample calling

- single sample calling repeated multiple times

- single sample calling on a merge of multiple samples (provided I remove read groups as I get "Warning: Multiple sample names (@RG:SM) present in the BAM file!" otherwise)

Thanks

d

[Tobias Rausch]

Hi,

Delly requires about 10,000 properly aligned pairs for every sample. That's the same for single-sample or multi-sample calling, it is a per-sample quality check. You can, of course, pool samples (merge BAMs) then Delly regards this as one sample.

Best, Tobias

 

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