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gavinha / TitanCNA

Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
GNU General Public License v3.0
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where to find ichorCNA.R and pysam version #100

Open ryao-mdanderson opened 11 months ago

ryao-mdanderson commented 11 months ago

Dear author @gavinha

I have two questions:

  1. Section : Scripts and Executables, where to find ichorCNA.R? ichorCNA.R (ichorCNA tool for normalizing and correcting read coverage)

  2. TitanCNA/scripts/snakemake/code/countPysam.py does not work with pysam version 0.21.0 I installed the application as a conda enviroment, I am not able to install pysam version 0.11.2.1 , Is any workaround?

    $ python scripts/snakemake/code/countPysam.py --help Traceback (most recent call last): File "$HOME/TitanCNA/scripts/snakemake/code/countPysam.py", line 7, in norm_hetpsns = sys.argv[2] IndexError: list index out of range

Thanks, Rong Yao