I'm a rookie in NGS analysis. I have several patients who have been studied in other centers: targeted panels, clinical exome or WES. The problem is that in some cases, the analysis of these studies did not include CNVs. Is it posible from the generated files (vcf, fastq) analyze if there is any CNV in those samples?. Thank you very much for your help. Kind regards, Javier
Have you tried searching the site/search online in general?
Align the fastq files against the reference genome - BWA or similar against GRCh.v.38 (or 37) - you might want to run the full GATK best practices pipeline. If the sequencing was all done as part of a batch (same flowcells, same library prep) you can run something like ExomeDepth or XHMM (read depth based callers) / Breakdancer (read-pair) / GATK 4 GermlineCNVCaller. Adjust for false positives either by checking against known sample CNVs (for example GIAB CNV calls on NA12878 or Ashkenazim Trio) and/or common batch specific CNVs.