Gavin Ha

Hi @2075222 This error is related to the incompatibility of the normal panel with the input wig files. `2923 elements in value to replace 1382 elements` Can you make sure...

Hi Luca, This is likely due to an incompatible or incorrect solution. Data points that have extreme values in the negative direction may sometimes be label-swapped in the prediction because...

Would be good to hear about your results after trying out a few of these parameter changes. You'll want to use `--includeHOMD True` if you do anticipate HOMD events such...

Hi @andreykoch I have included GC and map wig files for 50kb and 10kb. For the normal panel, unfortunately, the ultra-low coverage (0.1x) is not sufficient to generate a panel...

Hi @AgaricX We have built-in a check on the chromosomes of the input data to be specifically human. As you can see from `BSgenome.Hsapiends.UCSC.hg19` corresponds to Homo sapiens. You can...

Hi @hw538 Label switching has occurred. Very likely this is a suboptimal solution and should not be selected as the final result. I would recommend that you turn on the...

Hi @lbeltrame Sorry for the massively delayed follow up to this. Thank you for bringing up this great idea. We are currently considering incorporating something like this. Will keep you...

Hi @yuanzhao0502 1. The `coverage` field in the parameter file is hard-coded to report what you specify as coverage to the script. It is a legacy feature and not used...

Hi, Are you using ichorCNA for whole genome or whole exome sequencing data? If it's exome, then you will definitely need a matched normal. This can have a major effect...

Hi @ury This is unexpected and I wonder if it may be due to inclusion of some alt contigs/decoys in the WIG file. If this is still a problem for...