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’ ]

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’ ]

meta3 (map)

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

meta4 (map)

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

meta5 (map)

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

tumorbam (file)

Tumor or metastatic sample, BAM, SAM or CRAM file

*.{bam,cram,sam}

tummorbai (file)

Index

*.{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}

bwa_index (file)

BWA genome index files

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

fasta (file)

FASTA file

*.{fasta|fa}

fasta_fai (file)

Index of FASTA file

*.{fai}

dbsnp (file)

VCF file including dbSNP variants

*.vcf.gz

dbsnp_tbi (file)

Index of VCF file including dbSNP variants

*.vcf.gz.tbi

regions (file)

Targeted intervals. Accepts BED file or Samtools-style string

*.bed|*.txt|*.tab

Output

Name (Type)
Description
Pattern

meta (map)

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

versions (file)

File containing software versions

versions.yml

sv (file)

Filtered SVs for tumor only cases

*.vcf.gz

indel (file)

Filtered Indels for tumor only cases

*.vcf.gz

som_sv (file)

Somatic filtered SVs for tumor/normal paired samples

*.vcf.gz

som_indel (file)

Somatic filtered Indels for tumor/normal paired samples

*.vcf.gz

germ_sv (file)

Germline filtered SVs for tumor/normal paired samples

*.vcf.gz

germ_indel (file)

Germline filtered Indels for tumor/normal paired samples

*.vcf.gz

unfiltered_sv (file)

Unfiltered SVs for tumor only cases

*.vcf.gz

unfiltered_indel (file)

Unfiltered Indels for tumor only cases

*.vcf.gz

unfiltered_som_sv (file)

Unfiltered somatic SVs for tumor/normal paired samples

*.vcf.gz

unfiltered_som_indel (file)

Unfiltered somatic Indels for tumor/normal paired samples

*.vcf.gz

unfiltered_germ_sv (file)

Unfiltered germline SVs for tumor/normal paired samples

*.vcf.gz

unfiltered_germ_indel (file)

Unfiltered germline Indels for tumor/normal paired samples

*.vcf.gz

raw_calls (file)

Raw, unfiltered variants

*.txt.gz

discordants (file)

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

*.txt.gz

log (file)

Log file

*.txt.gz