Navigating Data Integration Challenges

I’ve been diving into the complexities of integrating genomic data across different platforms lately. Specifically, I’m struggling with harmonizing variant datasets from GATK and Strelka outputs. How do you all approach ensuring data consistency and accuracy during this integration phase? Any insights or tools you find particularly helpful would be great.

‌⁠‍⁠​‍​‍‌⁠‌​​‍​‍​⁠‍‍​‍​‍‌‍‌⁠‌‍​‍‌⁠‌​‌‍‍‍​‍​‍​‍⁠​​‍​‍‌‍‍⁠​‍​‍​⁠‍‍​‍​‍‌‍⁠‍‌‍‌‌‌⁠‌⁠‌‌⁠⁠‌⁠‌​‌‍⁠⁠‌⁠​​‌‍‍‌‌‍​⁠​‍​‍​‍⁠​​‍​‍‌‍‍‌‌‍‌​​‍​‍​⁠‍‍​‍​‍‌‍⁠‍‌‍‌‌‌⁠‌⁠​‍​‍​‍⁠​​‍​‍‌‍‌​​‍​‍​⁠‍‍​‍​‍​⁠​‍​⁠​​​⁠​‍​⁠‌‍​⁠​​​⁠‌⁠​⁠​‌​⁠​⁠​‍​‍​‍⁠​​‍​‍‌‍‍​​‍​‍​⁠‍‍​‍​‍‌​‌‌‌‍⁠‌‌‍​‌‌⁠‌​‌‍‌‌‌​⁠‍‌​‍​​⁠‍​‌‌​‍‌‍‌​‌​‍⁠‌​⁠⁠‌‍‍​‌​‍⁠‌⁠​⁠‌⁠‍‌​‍​‍‌⁠⁠‌​