Warning message

[diegomd90]

Hello;

Thank you for developing this tool.

I got a Warning message from my sample:

cyrius -m bam_manifest.txt -g 38 -t 20 -p genome_cyp2d6 -o genome_cyp2d6
INFO:root:Processing sample deduped at 2023-10-29 20:35:41.743280
WARNING:root:Sample deduped has uneven coverage. CN calls may be unreliable.

Warning is self explanatory but I was wondering if there was anything I could get an output regardless.

[xiao-chen-xc]

Hi @diegomd90, it's just a warning. Cyrius will still try to make a call, i.e. output files will be produced. If you get a no-call in the output, that indicates that Cyrius cannot derive a confident call from your data.

[diegomd90]

Hello Xiao.
My TSV is empty so Im guessing no confidents calls were made...
Is there something I can do on the mapping step? Maybe tweak some parameters on BWA to get more reads on CYP2D6 locus??

Thx

[xiao-chen-xc]

If the tsv is empty, there must have been an error. Would you mind pasting the full output message here?