Filtering the vcf file
I'm wondering how snpgap and indelgap work. Let's say snpgap 1 indelgap 10, and the second question, do I understand correctly that max-idepth takes the average coverage of a variant in a sample, and if it is higher than the threshold that I set, it will not call it? If I have one sample and a threshold of, for example, 7000, then all variants with coverage greater than 7000 will not be called? And if I have two samples, in one of which the coverage of a variant is 6000 and in the other of the same variant 10000, then it will not be called in both cases?
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I hope this may help:
what is the properties of filtering the vcf files
For the depth part, let us assume we used the following command
bcftools view --max-depth 500 input.vcf, any variant where the depth for an individual exceeds 500 will be filtered out. This can be useful to avoid sites with unusually high coverage, which may indicate problematic regions, such as repetitive sequences or alignment artifacts.I understand how max-depth works, but I asked about max-idepth, indelgap and snpgap