A typical error message could look like this: /Users/moxu/xbin/seq/bcftools/plugins/gtc2vcf.so:ĭlopen. You should get a reason for why the plugin is not loading. $ bcftools +/Users/moxu/xbin/seq/bcftools/plugins/gtc2vcf.so -vv $ bcftools plugin /Users/moxu/xbin/seq/bcftools/plugins/gtc2vcf.so -vv (a bcftools plugin bug that the maintainers will fix soon), can you try to run one of the following commands instead: $ bcftools plugin gtc2vcf -vv Run "bcftools plugin -lv" for more detailed error output.
#BCFTOOLS INSTALL INSTALL#
To install we first need to download and extract the source code with curl and tar respectively. If you get the error: No functional bcftools plugins were found inīCFTOOLS_PLUGINS="/Users/moxu/xbin/seq/bcftools/plugins". BCFtools is an open source program for variant calling and manipulating files in Variant Call Format (VCF) or Binary Variant Call Format (BCF). I would advise either to compile from source ( ) or alternatively to download pre-compiled binaries ( ) that should work on systems with ≥GLIBC_2.3 installed (and making sure you are running the latest version of BCFtools) I would advise (as of ) not to use the bcftools-gtc2vcf-plugin as it is an old version missing many features compared to the current version. .and install HTSlib to get these utilities, or see the additional instructions in INSTALL to install them from a samtools or bcftools source package. To search for alternate channels that may provide the conda package you'reĪnd use the search bar at the top of the page.
In this case, a lower version than would normally be installed if samtools were installed by itself. Forcing the installation of a specific version of openssl. PackagesNotFoundError: The following packages are not available from current channels: Instead the correct command is actually: conda install -c bioconda samtools bcftools openssl1.0 There are 2 different things going on in this command. Retrying with flexible solve.Ĭollecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Or conda install -c bioconda bcftools-gtc2vcf-pluginĪs instructed at, I got errors as follows: Collecting package metadata (current_repodata.json): done However, when I tried conda install bcftools-gtc2vcf-plugin All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. The source code releases are available from the download page. SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. Unzip the downloaded file to current location: o ' tar -jxvf bcftools-1.9.tar. BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. As time permits, this information will be updated for the new samtools/bcftools versions and moved to the new website.Download from the authors website: o ' wget.I have installed bioconda following the instructions at. Go to where you want to install: o ' cd /gpfs1/home/ USERNAME/SOFTWARE'.
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