Description

Rapid haploid variant calling

Input

Name (Type)
Description
Pattern

meta (map)

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

]

reads (file)

List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.

*.{fq,fastq,fq.gz,fastq.gz}

index (file)

Reference genome in GenBank (preferred) or FASTA format

*.{gbk,gbk.gz,fa,fa.gz}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

tab (file)

A simple tab-separated summary of all the variants

*.tab

csv (file)

A comma-separated version of the .tab file

*.csv

html (file)

A HTML version of the .tab file

*.html

vcf (file)

The final annotated variants in VCF format

*.vcf

bed (file)

The variants in BED format

*.bed

gff (file)

The variants in GFF3 format

*.gff

bam (file)

The alignments in BAM format. Includes unmapped, multimapping reads. Excludes duplicates.

*.bam

bai (file)

Index for the .bam file

*.bam.bai

log (file)

A log file with the commands run and their outputs

*.log

aligned_fa (file)

A version of the reference but with - at position with depth=0 and N for 0 < depth < —mincov (does not have variants)

*.aligned.fa

consensus_fa (file)

A version of the reference genome with all variants instantiated

*.consensus.fa

consensus_subs_fa (file)

A version of the reference genome with only substitution variants instantiated

*.consensus.subs.fa

raw_vcf (file)

The unfiltered variant calls from Freebayes

*.raw.vcf

filt_vcf (file)

The filtered variant calls from Freebayes

*.filt.vcf

vcf_gz (file)

Compressed .vcf file via BGZIP

*.vcf.gz

vcf_csi (file)

Index for the .vcf.gz via bcftools index

*.vcf.gz.csi

txt (file)

Tab-separated columnar list of statistics

*.txt
author
Github user rpetit3
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

snippy
GPL v2

Rapid bacterial SNP calling and core genome alignments

github.com/tseemann/snippy