sequencing-coverage

Compute BAM sequencing coverage using samtools

usage

nexus run --nf-workflow utilities_sequencing-coverage.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/

Note

Nextflow config files are available here. Use the config file that matches your installed nexus version (e.g. nexus_v0.2.0_nextflow_slurm.config).

parameters

parameter	description
--samples_tsv_file	TSV file with the following columns: ‘sample_id’, ‘bam_file’, ‘bam_bai_file’.
--output_dir	Directory to which output files will be copied.
--min_mapping_quality	Minimum mapping quality (default: 20).
--min_base_quality	Minimum base quality (default: 20).