Hi,
I'm working on filtering variants from a gene panel for schizophrenia genomics data (95 subjects), and I'd love your input on my approach. Current filtering criteria:
MIN(FORMAT/DP) > 10 && QUAL > 30
Available fields:
AO: Alt observation count QA: Quality of alt call RO: Reference observations count QR: Reference quality of call DP (from FORMAT) QUAL
Questions:
Are these filtering criteria sufficient for a focused gene panel in schizophrenia research?
How can I improve this filtering strategy given the available fields?
Should I incorporate AO, QA, RO, or QR into my filtering? If so, how?
I'm particularly concerned about striking the right balance between stringency and sensitivity. Any suggestions for refining this approach would be greatly appreciated.
Thank you for your time
