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Hi all - I'm a bit lost and need some guidance. I have WGS data from 2 twins. I want to compare the SNPs between the two twins in certain regions. So far, I've mapped the data using BWA and recalibrated it using GATK.
Now for calling SNPs in these regions, I've looked at the literature and there is a whole bunch of different tools that can do this, but each one seems to require data in different formats or doesn't accomplish quite what I need. Has anyone gone through this and is willing to share what they did?
Now for calling SNPs in these regions, I've looked at the literature and there is a whole bunch of different tools that can do this, but each one seems to require data in different formats or doesn't accomplish quite what I need. Has anyone gone through this and is willing to share what they did?