I have done a SNPs analysis and now I have a VCF.
I would like to filter it but I don't know what is usually done. For instance I know that I can filter by:
- Remove samples that have > x% missing data
- Remove SNPs that have > x% missing data
- Remove SNPs with >x% MAF
Do you have have other recommendation?
And also what are the standard parameters (x %) ?
Thanks for your help.