Comments (1)
J35P312
commented on August 20, 2024
Hello there!
the AMYCNE call module is a bit shaky, I'm developing it mostly as a side project, so proceed with caution!
The GC file looks fine. The coverage file might need some fixing:
I would start by removing the meanCoverage, and sampleName column.
The accepted columns (tab separated) are:
chromosome,start,end,coverage
or
chromosome,start,end,coverage,per_bin_quality_score
AMYCNE call is only tested on 30X human whole genomes. If the coverage is low, you may need to change the --s_cutoff limit.
Mostly, I'm still using CNVnator - I found these tools to perform similarily on 30X data. Feel free to give AMYCNE call a try, otherwise, I would reccomend you to try CNVnator!
Good luck!
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