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

Github user kubranarci
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