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

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

vcf fastq clinvar annovar
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updated by colindaven colindaven • written by nanibito • nanibito

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

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written by colindaven colindaven

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