I have a filter file , it was filtered based on low quality<11 , indelGap , snpgap.
First, why they choose the threshold 11 ?
Second, what is the meaning of snpgap and IndelGap ?
Finally, is there any way or evidence that tells me the data should be filtered or not or this data had enough filtering.
I am a statistician, i need to know about these kind of things, if there is a paper or book can help me more in vcf tools and format, it will be helpful.