How to preprocess, normalize, decompose a VCF file before inputting to the SNPEff? Heard, people use -sed and -grep to process VCFs somehow.
Yes you can use sed and grep. For a more detailed answer, please add some context to your question.
There is a "cant find chromosome error" in SNPEff output see VCF`s headers C: How to reduce annotation errors using SNPEff on BBMap`s and Pilon`s VCFs?. What
exactly commands can fix that? thank you
I don't get the point about what you are exactly looking for, but bcftools is always a nice option for VCF processing.