Gavin Ha

Hi @yuanzhao0502 I used Picard `DownSampleSam`. I also made sure to downsample a BAM that has duplicates removed. The `readCounter` tool in the ichorCNA pipeline ignores duplicates and sampling duplicate...

Hi @CuriusScientist Are you referring to additional bin sizes for the normal panel? We provide the gc and map wig files for 50kb and 10kb so you could ignore the...

Hi Albert, This is a good point. The `wigToRangedData` function is a HMMcopy R/Bioconductor function. We can try to better catch this error and output an appropriate error message. Thanks...

Hi @zhangyafeng1 , Please do a git pull of this repo and you will have the scripts. In the snakemake `config.yaml`, you can point to the R scripts that you...

Hi @ArshiyaG ichorCNA can be used for tumor-only mode. I am not able to comment on your issue without additional information. Best, Gavin

Hi @ArshiyaG ichorCNA runs on tumor-only mode by default. Of course, including a normal sample will improve the analysis. There are several reasons for discrepancies between tumor-normal vs tumor-only. The...

Hi @JJMaggie The sample should be male? Here is the argument you can use to tweak the setting for gender determination. https://github.com/broadinstitute/ichorCNA/blob/8021afa5b72f34e8fce3c30efe0bcae9f735122d/scripts/runIchorCNA.R#L47 This argument specifies the minimum proportion of reads...

Hi @seedgeorge We still need to add this flexibility to the R script but for now you can make some minor adjustments to hardcode the sex/gender. Here are the relevant...

Hi @jfrigola Yes, you can use ichorCNA for tumor samples as well. Best, Gavin

Hi @2075222 We provide one example file (without matched normal) here: https://github.com/broadinstitute/ichorCNA/blob/master/inst/extdata/MBC_315.ctDNA.reads.wig With regards to your error, I believe there may be issues with the format of your wig file....