How To Interpret The Parameters In Somatic Sniper

Question

[kulkarni.aishwarya87]

Hi , I am new to using somatic sniper . I have been going through the parameters and I cannot quiet get the following parameters:

-T     FLOAT theta in maq consensus calling model (for -c/-g) [0.850000]

I tried looking for this parameter on the MAQ website but it has no explanation

-N     INT number of haplotypes in the sample (for -c/-g) [2]
-r     FLOAT prior of a difference between two haplotypes (for -c/-g) [0.001000]

Thanks a lot!

Answer 1

[ernfrid]

I'm having trouble finding that information as well. All of these parameters are a straight pass through from the MAQ consensus calling model.

Theta in this case is a downweighting of evidence to help account for error correlation across reads. It is described in the "Consensus genotype calling" methods part of the MAQ paper (http://genome.cshlp.org/content/18/11/1851.full). r is also described in the same section.

I can't recall a good description of the handling of haplotypes, but the option was exposed in the SomaticSniper command line in case anyone wanted to use it.

Answer 2

[kulkarni.aishwarya87]

Thanks a lot! that was very helpful.. I shall go through that..