GATK CalculateContamination - zeros in output
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Entering edit mode
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 :)

GATK CalculateContamination MuTect2 • 449 views
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Entering edit mode
7 months ago

If you used GATK GetPileupSummaries, did you use a VCF/interval list file that would have positions your input BAM would cover?

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

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