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compare VQSR between two cohorts: same WES different designs

manolismanolis Member ✭✭


to run VQSR I need to have at least 30 WES... Up to date I used WES data with ~50-60Mb target region (intervals). Now I have 30 new WES ran with a 33Mb target design (CCDS regions). I saw in old posts that there is not a real cut off (minimum number of variants)... and on the other hand if you do not have enough data/variants you will have an error (or warning, I do not remember).

If I want to compare the overall "quality" of the VQSR recalibration between 30 WES with ~50-60Mb design and the same 30 WES previously analyzed (preProcessing/HaplotypeCaller) with the 33Mb desing , how can I do it or what VQSR value/data I need to use? I do not want to compare the vcf files.

Many thanks


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