Small clarification regarding --minPosterior option

[Venitha Bernard]

Hello.

I would like to filter variants while running Platypus based on QUAL and DP. I have two sets of samples. I want to filter one with QUAL >= 20 and DP >= 20 and the other one as QUAL >= 60 and DP >= 7

I am confused whether or not to use the --minPosterior option. Is it actually the same as the phred-scaled genotype posterior probabilities GP/PP? Or is it just filtering based on QUAL? 

I also noticed that variants with QUAL less than 20 by default fail the Q20 filter. Would you advice changing this parameter in the script manually?

[Andy Rimmer]

Hi,

the --minPosterior threshold determines which variants are output to the VCS. Anything with PP < minPosterior will not be included in the VCF. The value used is the QUAL value.

It's probably easier to filter on QUAL and DP from the VCF, rather than setting parameters in Platypus. 

Kind regards,

Andy

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Dr Andrew (Andy) Rimmer