Analyse variants from nanopore reads ==================================== Apply the variant calling pipeline to reads from Nanopore sequencer. Purpose ------- * Analyse variants in Nanopore reads Required inputs --------------- * Single-end reads from Nanopore sequencer in gzipped fastq format * Each sample is represented by a single gzipped fastq file * Reference genome in fasta format :: |-- reads/original |-- .fastq.gz |-- .fastq.gz |-- reference/ |-- .fa Generated outputs ----------------- * List of identified variants in VCF file, filtered by user-defined criteria * Summary PDF report to assess quality of reads, mapping and variant calling Example ------- How to run example: .. code-block:: bash cd /usr/local/snakelines/example/nanopore snakemake \ --snakefile ../../snakelines.snake \ --configfile config.yaml \ --use-conda Example configuration: .. literalinclude:: ../../example/nanopore/config.yaml :language: yaml