I am new to exome-seq and would be grateful for any suggestions :)
I want to run GATK CalculateContamination (GATK 220.127.116.11), before calling variants with MuTect2. CalculateContamination tool returns "SUCCESS" message, but with warnings, and I get only "0" values in my output file :
sample contamination error my_sample 0.0 0.0
Here are warnings after running GATK CalculateContamination:
WARN KernelSegmenter - Number of points needed to calculate local changepoint costs (2 * window size = 100) exceeds number of data points (12). Local changepoint costs will not be calculated for this window size. WARN KernelSegmenter - No changepoint candidates were found. The specified window sizes may be inappropriate, or there may be insufficient data points. INFO KernelSegmenter - Found 0 changepoints after applying the changepoint penalty. WARN KernelSegmenter - Specified dimension of the kernel approximation (100) exceeds the number of data points (12) to segment; using all data points to calculate kernel matrix.
Here is my code:
gatk CalculateContamination \ -I GetPileupSummaries_output.table \ -O CalculateContamination_output.contamination.table
I searched GATK documentation but didn't find any instructions there. I will be most grateful for any help :)