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nf-core/hiphase @ 0.0.0-6c4ed3a

Small and structural variant phasing tool for PacBio HiFi reads, supporting co-phasing of SNVs and SVs across multiple BAM files and samples

pacbio structural variant phasing pacbio hifi snv haplotagging
Latest version: 0.0.0-6c4ed3a
Total downloads: 2
Source: nf-core/modules
Authors: @tanyasarkjain @fellen31
Maintainers: @fellen31

Summary

Small and structural variant phasing tool for PacBio HiFi reads, supporting co-phasing of SNVs and SVs across multiple BAM files and samples

Get started

Add the following snippet to your workflow script to include this module.

include { HIPHASE } from 'nf-core/hiphase'

License

MIT License

Process
Name HIPHASE
Input 8 channels
#1 tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
bams file

One or more sorted BAM/CRAM files

 *.{bam,cram}
bais file

Index files associated with the BAM/CRAM files

 *.{bai,crai,csi}
snv file

Compressed VCF file containing SNV/small variants to phase (optional)

 *.{vcf.gz}
snv_index file

Index file for the SNV VCF (optional)

 *.{tbi,csi}
sv file

Compressed VCF file containing structural variants to co-phase (optional)

 *.{vcf.gz}
sv_index file

Index file for the SV VCF (optional)

 *.{tbi,csi}
samples list

List of sample names to phase within the VCF, if empty only the first sample is phased.
#2 tuple
meta2 map

Groovy Map containing reference genome information e.g. [ id:'GRCh38' ]
fasta file

Reference genome FASTA file used for the BAM alignment

 *.{fasta,fa}
fai file

FASTA index file (.fai) for the reference genome

 *.fai
output_bam boolean

Whether to output haplotagged BAM files. Set to true to emit phased BAM files with haplotag information.
summary_file boolean

Whether to output a phasing summary file.
blocks_file boolean

Whether to output a phasing blocks file.
stats_file boolean

Whether to output a per-read phasing statistics file.
haplotag_file boolean

Whether to output a haplotag assignments file.
file_format string

Output file format for summary/blocks/stats/haplotag files, either 'tsv' or 'csv'.
Output 15 channels
#1 bams tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
*.bam file

Haplotagged BAM file(s) with haplotype information in the HP tag (optional, only emitted when output_bam is true)

 *.bam
#2 vcfs tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
*_snv_phased.vcf.gz file

Phased and compressed SNV VCF file (optional, only emitted when SNV VCF input is provided)

 *_snv_phased.vcf.gz
#3 sv_vcfs tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
*_sv_phased.vcf.gz file

Phased and compressed SV VCF file (optional, only emitted when SV VCF input is provided)

 *_sv_phased.vcf.gz
#4 stats_csv tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
*.stats.csv file

CSV file containing per-read phasing statistics (optional)

 *.stats.csv
#5 stats_tsv tuple
meta map