When I used the cnvkit.py sex command to infer sample sex, for some of my samples the results (Male/Female) was different depending on whether the .cnr or the .cns file was used as input, although the X and Y log2 ratios were practically the same.
An example output is as follows, where the results for sample s1 were consistent, but the results for sample s2 were not between cnr and cns -- in this case, the cns result is apparently wrong. The default "female reference" was used throughout the analysis.
sample sex X_logratio Y_logratio
s1.cnr Male -1.02 +0.255
s1.cns Male -1.02 +0.255
s2.cnr Male -1.03 +0.236
s2.cns Female -1.03 +0.235
I discovered this issue when I used the cns files for cnvkit.py heatmap and the X chromosome log2 ratio for some samples did not look right, and the log file also revealed some incorrect sex inference; however, messages about sex inference in the logs files of cnvkit.py batch (which I used to perform my analysis) was correct. I was initially using cnvkit 0.9.4. I tried the latest version to date (0.9.9, installed via anaconda) but the issue persisted.
I may have some difficulty sharing the relevant cns and cnr files due to restrictions of my institution... Please kindly let me know how I can help with further debugging, if necessary. Thanks.
When I used the
cnvkit.py sexcommand to infer sample sex, for some of my samples the results (Male/Female) was different depending on whether the .cnr or the .cns file was used as input, although the X and Y log2 ratios were practically the same.An example output is as follows, where the results for sample s1 were consistent, but the results for sample s2 were not between cnr and cns -- in this case, the cns result is apparently wrong. The default "female reference" was used throughout the analysis.
I discovered this issue when I used the cns files for
cnvkit.py heatmapand the X chromosome log2 ratio for some samples did not look right, and the log file also revealed some incorrect sex inference; however, messages about sex inference in the logs files ofcnvkit.py batch(which I used to perform my analysis) was correct. I was initially using cnvkit 0.9.4. I tried the latest version to date (0.9.9, installed via anaconda) but the issue persisted.I may have some difficulty sharing the relevant cns and cnr files due to restrictions of my institution... Please kindly let me know how I can help with further debugging, if necessary. Thanks.