GATK CalculateContamination – zeros in output

GATK CalculateContamination – zeros in output



I am new to exome-seq and would be grateful for any suggestions 🙂

I want to run GATK CalculateContamination (GATK, 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 🙂





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