Gavin Ha

Hi @ury @blackbeerd I think the problem is that you are using a slightly older version of ichorCNA. Can you please install the latest version in the repo (last updated...

Hi Sudhir, The exon/targeted interval file is used to select (via overlap) the bins from the WIG files. The normalization approach used by ichorCNA requires equal sized, non-overlapping bins; therefore,...

Hi @smangul1 This error usually occurs when there there are either (1) too few bins remaining after filtering or (2) the coverage is too low for the loess curve fitting....

Hi, There are potentially several theoretical problems with using 10Mb bins 1) GC content and mappability bias corrections are being performed on too few bins. I'm not even sure GC...

Hi @samhitapn For the centromere exclusion, if you provide a centromere gap file in the `config.yaml`, then it will perform the removal in the analysis. Otherwise, it will not. https://github.com/broadinstitute/ichorCNA/blob/5bfc03ed854f0e93fe5b624c97c1290fa0053837/scripts/snakemake/config/config.yaml#L19...

Hi @yuanzhao0502 You can find instructions to generate the reference gc and map files here: https://github.com/shahcompbio/hmmcopy_utils Best, Gavin

Hi @Haldrup @CuriusScientist Specifying chrY in `--chrs` should be the way to do it but I haven't tested it. I'll try to look into this. Best, Gavin

Hi @xin8you The reason it's failing for you is because the panel of normal you're using does not contain data for chrY and thus incompatible with the analysis of chrY....

Hi @grenaud What genome style are you using as input in the `congfig.yaml`?

Hi @TendoLiu At the moment, paired tumor-normal analysis is not supported by the snakemake pipeline here. You can consider (TitanCNA)[https://github.com/gavinha/TitanCNA], which uses ichorCNA as a pre-processing step and does use...