Hello,
I've used GATK to produce variant calls (VCF files). I have shallow coverage (<10) and the documentation suggests using 'Variant quality score recalibration' according to 'true sites' from HapMap 3 and Omni 2.5M SNP chip array. My question is, will I loose all the variants not occuring on those controls? For example, will I loose novel variant?
any advise on this is welcome
Thanks
Jorge
I've used GATK to produce variant calls (VCF files). I have shallow coverage (<10) and the documentation suggests using 'Variant quality score recalibration' according to 'true sites' from HapMap 3 and Omni 2.5M SNP chip array. My question is, will I loose all the variants not occuring on those controls? For example, will I loose novel variant?
any advise on this is welcome
Thanks
Jorge
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