Description

smoove simplifies and speeds calling and genotyping SVs for short reads. It also improves specificity by removing many spurious alignment signals that are indicative of low-level noise and often contribute to spurious calls. Developped by Brent Pedersen.

Input

name:type
description
pattern

meta:map

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

]

input:file

BAM/CRAM file

*.{bam,cram}

index:file

Index of BAM/CRAM file

*.{bai,crai}

exclude_beds:file

A BED file containing the regions to exclude from the SV calling

*.bed

meta2:map

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

]

fasta:file

The reference fasta file

*.{fasta,fna,fa}

meta3:map

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

]

fai:file

Index of reference fasta file

*.fai

Output

name:type
description
pattern

vcf

meta:map

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

]

*.vcf.gz:file

Compressed VCF file

*.vcf.gz

versions

versions.yml:file

File containing software versions

versions.yml

Tools

smoove
Apache-2.0

structural variant calling and genotyping with existing tools, but, smoothly

github.com/brentp/smoove brentp.github.io/post/smoove https://github.com/brentp/smoove
maintainers
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Github user nvnieuwk
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