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McGranahanLab / CONIPHER-wrapper

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'chr' prefix in the chromosome names in the input.tsv file seems to cause an error even though it should get handled according to the paper #6

Open stefmldk opened 7 months ago

stefmldk commented 7 months ago

Firstly: Thank you for making this tool! For anyone strictly using this repo as documentation to format their input.tsv file, this may not be an issue. For anyone also using the corresponding Nature Protocols paper, the following is written under the "Conventions" section: "Chromosome names can be either with or without the ‘chr’ prefix (e.g., ‘1’ or ‘chr1’)" However, including the 'chr' prefix actually causes the script to error out because at the step where chromosomes X and Y are filtered out, filtering is done by only including the numerical values 1-22. If 'chr' is used in the chromosome names, an empty table is produced. Best, Steffen

stefmldk commented 7 months ago

In relation to my previous comment, it should also be mentioned that the paper - also in the "Conventions" section - gives the impression that X and Y chromosomes get "ignored". But they should not be included in the input.tsv file as it will cause an error.