modules/svaba

SvABA is an efficient and accurate method for detecting SVs from short-read sequencing data using genome-wide local assembly with low memory and computing requirements

svstructural variantsdetecting svsshort-read sequencing

https://github.com/nf-core/modules/[...]/modules/nf-core/svaba

Description

SvABA is an efficient and accurate method for detecting SVs from short-read sequencing data using genome-wide local assembly with low memory and computing requirements

Input

name:type

description

pattern

`meta:map`

Groovy Map containing sample information id: should be the identification number or sample name. If there is normal file meta should be common e.g. [ id:‘test’ ]

`tumorbam:file`

Tumor or metastatic sample, BAM, SAM or CRAM file

*.{bam,cram,sam}

`tumorbai:file`

Index of the tumor or metastatic sample

*.{bai,crai,sai}

`normalbam:file`

Control (or normal) of matching tumor/metastatic sample, BAM, SAM or CRAM file

*.{bam,cram,sam}

`normalbai:file`

Index

*.{bai,crai,sai}

`meta2:map`

Groovy Map containing FASTA information id: should be the identification number for alignment file and should be the same used to create BWA index files e.g. [ id:‘fasta’ ]

`fasta:file`

FASTA file

*.{fasta|fa}

`meta2:map`

Groovy Map containing FASTA information id: should be the identification number for alignment file and should be the same used to create BWA index files e.g. [ id:‘fasta’ ]

`fasta_fai:file`

Index of FASTA file

*.{fai}

`meta3:map`

Groovy Map containing BWA information id: should be the identification number same as fasta file e.g. [ id:‘bwa’ ]

`bwa_index:file`

BWA genome index files

Directory containing BWA index *.{amb,ann,bwt,pac,sa}

`meta4:map`

Groovy Map containing dbSNP information id: should be the identification number for dbSNP files e.g. [ id:‘test’ ]

`dbsnp:file`

VCF file including dbSNP variants

*.vcf.gz

`meta4:map`

Groovy Map containing dbSNP information id: should be the identification number for dbSNP files e.g. [ id:‘test’ ]

`dbsnp_tbi:file`

Index of VCF file including dbSNP variants

*.vcf.gz.tbi

`meta5:map`

Groovy Map containing regions information id: should be the identification number for regions e.g. [ id:‘test’ ]

`regions:file`

Targeted intervals. Accepts BED file or Samtools-style string

*.bed|*.txt|*.tab

Output

name:type

description

pattern

`sv`

`meta:map`

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

`*.svaba.sv.vcf.gz:file`

Filtered SVs for tumor only cases

*.vcf.gz

`indel`

`meta:map`

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

`*.svaba.indel.vcf.gz:file`

Filtered Indels for tumor only cases

*.vcf.gz

`germ_indel`

`meta:map`

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

`*.svaba.germline.indel.vcf.gz:file`

Germline filtered Indels for tumor/normal paired samples

*.vcf.gz

`germ_sv`

`meta:map`

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

`*.svaba.germline.sv.vcf.gz:file`

Germline filtered SVs for tumor/normal paired samples

*.vcf.gz

`som_indel`

`meta:map`

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

`*.svaba.somatic.indel.vcf.gz:file`

Somatic filtered Indels for tumor/normal paired samples

*.vcf.gz

`som_sv`

`meta:map`

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

`*.svaba.somatic.sv.vcf.gz:file`

Somatic filtered SVs for tumor/normal paired samples

*.vcf.gz

`unfiltered_sv`

`meta:map`

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

`*.svaba.unfiltered.sv.vcf.gz:file`

Unfiltered SVs for tumor only cases

*.vcf.gz

`unfiltered_indel`

`meta:map`

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

`*.svaba.unfiltered.indel.vcf.gz:file`

Unfiltered Indels for tumor only cases

*.vcf.gz

`unfiltered_germ_indel`

`meta:map`

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

`*.svaba.unfiltered.germline.indel.vcf.gz:file`

Unfiltered germline Indels for tumor/normal paired samples

*.vcf.gz

`unfiltered_germ_sv`

`meta:map`

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

`*.svaba.unfiltered.germline.sv.vcf.gz:file`

Unfiltered germline SVs for tumor/normal paired samples

*.vcf.gz

`unfiltered_som_indel`

`meta:map`

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

`*.svaba.unfiltered.somatic.indel.vcf.gz:file`

Unfiltered somatic Indels for tumor/normal paired samples

*.vcf.gz

`unfiltered_som_sv`

`meta:map`

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

`*.svaba.unfiltered.somatic.sv.vcf.gz:file`

Unfiltered somatic SVs for tumor/normal paired samples

*.vcf.gz

`raw_calls`

`meta:map`

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

`*.bps.txt.gz:file`

Raw, unfiltered variants

*.txt.gz

`discordants`

`meta:map`

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

`*.discordants.txt.gz:file`

Information on all clusters of discordant reads identified with 2+ reads

*.txt.gz

`log`

`meta:map`

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

`*.log:file`

Log file

*.txt.gz

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

svaba
GPL v3

Structural variation and indel detection by local assembly

github.com/walaj/svaba ncbi.nlm.nih.gov/pmc/articles/PMC5880247 https://github.com/walaj/svaba 10.1101/gr.221028.117