hapcut2-whatshap

Phase small variants with HapCUT2 and haplotag long-read DNA sequencing BAM files using WhatsHap

usage

nexus run --nf-workflow haplotagging_hapcut2-whatshap.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --reference_genome_fasta_file /path/to/file.fasta \
    --read_technology "pacbio" \
    --params_extracthairs "" \
    --params_hapcut2 "" \
    --params_whatshap_haplotag "--ignore-read-groups --skip-missing-contigs --output-threads 4"

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’ (VCF may be plain ‘.vcf’ or ‘.vcf.gz’)
--output_dir	Directory to which output files will be copied.
--reference_genome_fasta_file	Reference genome FASTA file.
--read_technology	Read technology for extractHAIRS (choices: pacbio, ont, illumina; default: ‘pacbio’).
--params_extracthairs	Extra extractHAIRS parameters (default: ‘““’). Note that the parameters need to be wrapped in quotes.
--params_hapcut2	Extra HAPCUT2 parameters (default: ‘““’). Note that the parameters need to be wrapped in quotes.
--params_whatshap_haplotag	Whatshap ‘haplotag’ parameters (default: ‘“--ignore-read-groups --skip-missing-contigs --output-threads 4”’). Note that the parameters need to be wrapped in quotes.