Filtering VCF - minimal valid filter parametrs

Question

[Lukas]

Hi,

I've realized that I've been conducting my analysis using VCF files that only have a filter for QUAL > 1, without any post-calling filtration. After spending considerable time searching online, I'm feeling quite lost. I'm uncertain where to begin and how much filtering is necessary to ensure my analysis is sound, especially as I'm presenting this work as part of my master's degree program.

I'm seeking guidance on the easiest and most effective approach to properly prefilter VCF files to exclude potentially invalid variations. Specifically, I'm interested in understanding what filtering parameters are appropriate and what level of information is sufficient for presentation purposes. Currently, I'm confident in using a threshold of QUAL > 30, but I'm unsure about other necessary filtering criteria.

Any assistance or advice on where to find suitable filtering parameters and how to implement them would be greatly appreciated.

Thank you for your help.

Answer 1

[Pierre Lindenbaum]

see https://gatk.broadinstitute.org/hc/en-us/articles/360035890471-Hard-filtering-germline-short-variants

[Lukas]

Thank you so much. I think this is literally what i was looking for. You are lifesaver.