hiphase

Phase small and structural variants in long-read DNA sequencing BAM files using HiPhase

usage

nexus run --nf-workflow variant_phasing_hiphase.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --reference_genome_fasta_file /path/to/file.fasta

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_gz_file’, ‘small_variants_vcf_gz_tbi_file’, ‘structural_variants_vcf_gz_file’, ‘structural_variants_vcf_gz_tbi_file’.
--output_dir	Directory to which output files will be copied.
--reference_genome_fasta_file	Reference genome FASTA file.