Question: How do I determine the correct filtering threshold in VCFfilter after running FreeBayes
24 months ago by
jamieburke1020 • 0
jamieburke1020 • 0 wrote:
I would like to perform a VCFfilter on my FreeBayes data but I'm not sure how to choose the correct parameters for filtering. I visualized my variants with vcf.iobio. Where do I find the correct number from my data for the following fields: -f "DP > 10" # for info fields -g "GT = 1|1" # for genotype fields -f "CpG" # for 'flag' fields
ADD COMMENT • link •modified 23 months ago by chen.randy • 110 • written 24 months ago by jamieburke1020 • 0
Hello - I am not quite sure what the question is. Have you tried these filters and examined the results? Or are you unsure about how to enter them on the form? Thanks for the extra info, Jen, Galaxy team
My question should be: How do I use the VCFfilter to only include sites where the chance of a false positive call is 1 in 10,000 or better according to the VCF qual field? This is how the question was stated in one of steps for a project within Coursera.