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. Developed by Brent Pedersen.

Input

name:type
description
pattern

meta{:bash}

:map

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

input{:bash}

:file

BAM/CRAM file

*.{bam,cram}

index{:bash}

:file

Index of BAM/CRAM file

*.{bai,crai}

exclude_beds{:bash}

:file

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

*.bed

meta2{:bash}

:map

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

fasta{:bash}

:file

The reference fasta file

*.{fasta,fna,fa}

meta3{:bash}

:map

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

fai{:bash}

:file

Index of reference fasta file

*.fai

Output

name:type
description
pattern

vcf{:bash}

meta{:bash}

:map

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

*.vcf.gz{:bash}

:file

Compressed VCF file

*.vcf.gz

versions{:bash}

versions.yml{:bash}

: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
Github user scorreard
Github user nvnieuwk
get in touch
Ask a question on Slack Open an issue on GitHub