Description

A haplotype-based variant detector

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

input_1:file

BAM/CRAM/SAM file

*.{bam,cram,sam}

input_1_index:file

BAM/CRAM/SAM index file

*.{bai,crai}

input_2:file

BAM/CRAM/SAM file

*.{bam,cram,sam}

input_2_index:file

BAM/CRAM/SAM index file

*.{bai,crai}

target_bed:file

Optional - Limit analysis to targets listed in this BED-format FILE.

*.bed

ref_meta:map

Groovy Map containing reference information. e.g. [ id:‘test_reference’ ]

fasta:file

reference fasta file

.{fa,fa.gz,fasta,fasta.gz}

ref_idx_meta:map

Groovy Map containing reference information. e.g. [ id:‘test_reference’ ]

fasta_fai:file

reference fasta file index

*.{fa,fasta}.fai

samples_meta:map

Groovy Map containing meta information for the samples file. e.g. [ id:‘test_samples’ ]

samples:file

Optional - Limit analysis to samples listed (one per line) in the FILE.

*.txt

populations_meta:map

Groovy Map containing meta information for the populations file. e.g. [ id:‘test_populations’ ]

populations:file

Optional - Each line of FILE should list a sample and a population which it is part of.

*.txt

cnv_meta:map

Groovy Map containing meta information for the cnv file. e.g. [ id:‘test_cnv’ ]

cnv:file

A copy number map BED file, which has either a sample-level ploidy: sample_name copy_number or a region-specific format: seq_name start end sample_name copy_number

*.bed

Output

name:type
description
pattern

vcf

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.vcf.gz:file

Compressed VCF file

*.vcf.gz

versions

versions.yml:file

File containing software version

versions.yml

Tools

freebayes
MIT

Bayesian haplotype-based polymorphism discovery and genotyping