Basics: How do I generate a VCF file from a genome and annotate it with Clinvar

Question

[nanibito]

Some basic, probably naive questions:

How can I create fresh VCF files (snp, indel, cnv) from an individual genomic sequence (fastq, ...) and the current reference genome?

If not done in the same step, how do I annotate this with ClinVar or Annovar and other public databases?

Are there standalone software packages for this?

I am also interested in correlating the genome with GWAS studies.

Many thanks for your help -- John

[Pierre Lindenbaum]

How can I create fresh VCF files (snp, indel, cnv) from an individual genomic sequence (fastq, ...) and the current reference genome?

http://www.htslib.org/workflow.html

how do I annotate this with ClinVar

bcftools annotate

Annovar

https://annovar.openbioinformatics.org/en/latest/user-guide/startup/

[colindaven]

There are 1001 good tutorials for this. Google is your friend :-). Also please google your error messages.