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 ------------------------------------------------------------------------------ Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
