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Hi,
I am new in this field. I was working with the 1000 genome vcf files. There I have seen that they are showing Genotype Likelihood (GL) instead of SNP coverage or SNP quality. Can anybody tell me what is genotype likelihood and how to interpret it? As well as from which value of GL we can tell that the gentotype which is being called is the true one? (Like for SNP quality,the rule of thumb is that greater than 30 is good value)
Thanks
Mayukh
I am new in this field. I was working with the 1000 genome vcf files. There I have seen that they are showing Genotype Likelihood (GL) instead of SNP coverage or SNP quality. Can anybody tell me what is genotype likelihood and how to interpret it? As well as from which value of GL we can tell that the gentotype which is being called is the true one? (Like for SNP quality,the rule of thumb is that greater than 30 is good value)
Thanks
Mayukh