filter the vcf file based on genotype quality

Question

[mostafarafiepour]

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

[Ram]

based on genotype quality

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?

What is the best threshold

There is no "best threshold", it depends on what you're trying to do. Please give us more details on your goal.

What is the best path

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.