filter the vcf file based on genotype quality
Hi All,
I want to filter the vcf file based on genotype quality. What is the best threshold for it?
And what is the best path to doing the genotype quality filter?
Best Regard
Mostafa
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Every sample has a GQ field for every variant. How do you wish to filter GQ? Minimum across samples, not more than M samples with GQ < x, etc - what would your filter be?
There is no "best threshold", it depends on what you're trying to do. Please give us more details on your goal.
Again, depends. I'd recommend
bcftools, but it also depends on what you're trying to accomplish. Going by your questions, it seems like this is a VCF pre-processing/pipeline filter, so you could add that to GATK FilterVariants if applicable.Please explain your purpose and what you've tried so far.