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