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How can we identify between the missing SNP (because of insufficent coverage) and homozygotic SNPs

tanu06tanu06 CanadaMember

Hi,
I had 11 samples for which i ran GATK (BQSR and VQSR), is there any way to differentiate between missing SNP (because of insufficent coverage) and homozygotic SNPs
Thanking you in anticipation.

With regards,
Tanushree

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