This guide provides a step-by-step guide to 1) convert BAM files (i.e., public) to FASTQ; and 2) run the nextflow nf-core/sarek variant calling pipeline.
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Prepare copy and paste the code below into a file called environment.yml - Tip: use a text editor (i.e., vim, nano or other)
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conda env update --file environment.yml |
To deactivate the conda environment, run:
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conda deactivate |
Convert BAM to FASTQ
STEP1: install bedtools if this is not yet available
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