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I have HiSeq exome data, and using GATK v.2.5 While trying to do variant recalibration, I had got an error with default for -percentBad and --maxGaussians. Searching the forum, according to the tip that suggested to loosen those, increasing the first to 0.05 or decreasing the second to 4, the walker worked well. Actually either have been enough for one case of my data. However, for an other data, it finally worked when both were adjusted. Even, another case is being tested with more generous setting. The options that I have controlled are below: -minNumBad , -percentBad , --maxGaussians
What I wonder for options is, 1. Appropriate values could certainly differ sample by sample? ( Sometimes it's natural to try and adjust? ) 2. Are there known values with the most generous level to keep reasonable performance? ( To what extent is it safe to loose the values? )
Any comment much appreciated. Let me know if I missed some information. KIM