Input_file and annotation

[FL512]

Dear Palimpsest developer,

First of all, thank you very much for giving an opportunity to use a wonderful tool for mutational analysis. I am exciting to use this and hopefully I would get used to it soon.

I have questions, maybe this could be an inappropriate to post as issues, however, I should be happy if I get your feedback. Based on the previous response to the "preprocess input_snv error" and judging from the exercise dataset (vcf.RData), VCF file should have the following columns; https://github.com/FunGeST/Palimpsest#input-files.

1. How did you make them? Did you generate input dataset manually from vcf files? My vcf file does not have the required columns, so I got an error. Please find an attached screenshot.

2. What is the Tumor_Varcount? It states as "Number of variant bases at the position in the tumor sample" but how to get it?

Best regards,