Filter VCF data to merge with SNP array data - good filter settings?
I have VCF data from a publication from 108 genomes.
I also have Plink SNP data from the Human Origins array, and I want to merge in these VCF data into the Plink data.
What would be good settings for filtering SNPs. The VCF files have already been filtered for DP >= 10 and GQ >=30.
I don't have any genes/loci of interest - I just need to get overlapping SNP data. What other filtration settings should I use?
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