[Samtools-help] samtools variant calling on pedigree samples

[Amy W. <al...@co...>]

Hi,

I've got WGS data for several three-generation pedigees that I need to 
call variants on. I am also have some data for unrelated samples. There 
are two ways I'm considering calling variants with samtools:

1. All samples, including the closely related individuals together (N = 
~200 samples)

2. Run variant calling separately for each related individual but using 
the same set of unrelated samples in each case (N =~ 160 samples).

Option (2) will take more compute power, but I don't want to bias 
calling due to the relatedness, so I'm willing to do it.

My question is, will samtools be very biased by the relatedness of the 
samples? I would think that with sufficient numbers of unrelated 
individuals, it shouldn't matter much, it will likely affect things 
somewhat, no?

Any advice?

-Amy