VCF-kit
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VCF-kit: Assorted utilities for the variant call format
The current build of Muscle (5.1) as of 2022-08-25 doesn't have the command "-maketree". I tested with a previous version (muscle-3.8.1551) and everything works fine. I would suggest updating the...
Hi I am running vcf-kit (version 0.2.6) from a anaconda installation. I am trying to run the tajima module using the following command: `vk tajima 10000 10000 chromosme.vcf.gz > chromosome_td.tsv`...
Hi! I'm wondering if it is possible to use a genome assembly that cannot be downloaded with the available methods? I'm working with the Zostera marina assembly (PRJNA41721) and it...
Hello, I have been unable to successfully download and run vcfkit and have exhausted all options. I have tried the various install methods and even tried changing the primer3.py script...
Hi, I am trying to run Tajima's D in vcf-kit using the following command: **docker run -it andersenlab/vcf-kit vk tajima 10000 --sliding file.vcf** However, I receive the following set of...
Hello - I am receiving the following error using the latest docker image (andersenlab/vcf-kit:20200822175018b7b60d). Any idea what this means or what I need to do to fix it? Any help...
Hi, I am trying understand what is causing the warning "**Note: the --sample option not given, applying all records regardless of the genotype**". I don't see any options in the...
Hi, I am trying to build a tree based on a specific region on a chromosome - however I am receiving the error below saying that there was an issue...
Hello, I am having an environment.yml file and I am installing vcfkit through conda. The file looks as follows: name:myenv channels: - bioconda depedencies: -vcfkit I get the following error...