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8 months ago

wiki97
•
0

Hi,

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

I want to run GATK **CalculateContamination** (GATK 4.1.8.1), 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 :)

Yes, I used GATK GetPileupSummaries and I used an interval file, this file was output from GATK RealignerTargetCreator tool.