margin

Phase small variants and haplotag long-read DNA sequencing BAM files using Margin

usage

nexus run --nf-workflow haplotagging_margin.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --reference_genome_fasta_file /path/to/file.fasta \
    --margin_phase_params_json_file /path/to/file.json \
    --params_margin_phase ""

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’, ‘small_variants_vcf_file’
--output_dir	Directory to which output files will be copied.
--reference_genome_fasta_file	Reference genome FASTA file.
--margin_phase_params_json_file	Margin ‘phase’ HMM parameters JSON file. Pick a file matching your sequencing platform — sample fixtures ship at test/data/indices/margin/phase/, and the margin docker image carries the same set under /opt/margin/params/.
--params_margin_phase	Margin ‘phase’ extra arguments appended verbatim (default: ‘““’). Wrap in quotes.