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?