[Samtools-help] understanding bcftools -m (samtools 0.1.19)

I am trying out the new version (0.1.19) of samtools/bcftools for multisample calling, and in particular -m option for bcftools. However, I am struggling to work out what the float value should be, and what the ch^2 value in the description refers to.

-m FLOAT  alternative model for multiallelic and rare-variant calling, include if P(chi^2)>=FLOAT

I would be grateful for any insight into how to best select this parameter. For context I am multisample calling ~3000 high coverage exomes and don't want to miss singletons.

Many thanks

Michael

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Dr Michael Simpson
Genetics and Molecular Medicine
King's College London
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