Interpretting cnvkit p-value results
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Entering edit mode
11 months ago
tjbencomo ▴ 10

I'm using cnvkit to analyze several tumors sequenced via WGS without any normal controls. I've analyzed the samples with the following command

cnvkit.py batch RWRB*.tumor.bam \
-n -p $NCORES \
-f $PI_HOME/refs/hg38/Homo_sapiens_assembly38.fasta \
--annotate refFlat.txt \
--drop-low-coverage \
--output-reference chist_ref.cnn --output-dir results/ \
--method wgs \
--diagram --scatter

In the log files I see this warning for every sample:

Segmenting with method 'cbs', significance threshold 1e-06, in 1 processes
[...]
Significant hits in 0/582671 bins (0%)
Wrote results/RWRB9.tumor.bintest.cns with 0 regions

I'm not sure what Significant hits in 0/582671 bins means - does this mean none of the CNVs are significant? This would seem to contradict the results from the call command as looking at the output files with the call.cns extension show lots of significant results according to the p_ttest column

chromosome      start   end     gene    log2    cn      depth   p_ttest probes  weight
chr1    16949165        17609179        CROCCP2   -0.134326       2       32.6053 1.59541e-10     132     125.51
chr1    17609179        17699181        PADI3       0.241978        3       50.4047 2.69434e-07     18      17.1149

In fact 87% of the regions in the results file are significant at p < .05. What is the correct interpretation of these results?

cnvkit cnv • 430 views
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