What do the freebayes parameters --pooled-continuous/--pooled-discrete mean?
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2.9 years ago
markd ▴ 40

Hi all,

I'm looking for an explanation on the freebayes parameters --pooled-continuous/--pooled-discrete, but can't find it anywhere.

What do they do, and when should I use them?

SNP freebayes variant-calling next-gen • 2.2k views
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Did you read freebayes -h? It shows some information, though admittedly leave a lot of room for interpretation:

-J --pooled-discrete
               Assume that samples result from pooled sequencing.
               Model pooled samples using discrete genotypes across pools.
               When using this flag, set --ploidy to the number of
               alleles in each sample or use the --cnv-map to define
               per-sample ploidy.
-K --pooled-continuous
               Output all alleles which pass input filters, regardles of
               genotyping outcome or model.

However, there is plenty of further discussions / sources of information around, which should get you going:

https://groups.google.com/forum/#!topic/freebayes/KSHsQ-D_ems

https://wiki.metacentrum.cz/wiki/FreeBayes

https://groups.google.com/forum/#!topic/freebayes/sXhAuzV2MqU

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