Variants calling (VCF)
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3.0 years ago

I am new to ngs data analysis. I have the VCF file from targeted sequencing of 3 genes. How can i filter the variants using QUAL (phred score), GQ (genotype quality) and DP (read depth). What are the range of these parameters to get the confident variants out of hundreds of variants in VCF file.

ngs vcf • 891 views
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Hello,

have you tried to search for a program? If you would have, than you would have found at least bcftools and SnpSift.

Concerning your question about the ranges: Welcome to one of the most difficulty parts of ngs analysis. There are no fixed borders, because it depends heavily on what's the goal of your experiment, sequencing platform, library prep, bioinformatics pipeline, etc...

So if you tell us more about what you like to do, maybe one can give better recommondations.

fin swimmer

BTW: Hundreds of Variants in 3 genes? Realy?

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