Description

Gathers paired-end and split read evidence files for use in the GATK-SV pipeline. Output files are a file containing the location of and orientation of read pairs marked as discordant, and a file containing the clipping location of all soft clipped reads and the orientation of the clipping.

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/SAM file

*.{bam,cram,sam}

input_index{:bash}

:file

Index of the BAM/CRAM/SAM file

*.{bai,crai,sai}

site_depth_vcf{:bash}

:file

Optional - input VCF of SNPs marking loci for site depths, needed for the site depths output

*.vcf.gz

site_depth_vcf_tbi{:bash}

:file

Optional - input VCF TBI of SNPs marking loci for site depths, needed for the site depths output

*.vcf.gz.tbi

fasta{:bash}

:file

Optional - reference FASTA file needed when the input is a CRAM file

*.{fasta,fa}

fasta_fai{:bash}

:file

Optional - index of the reference FASTA file needed when the input is a CRAM file

*.fai

dict{:bash}

:file

Optional - sequence dictionary of the reference FASTA file needed when the input is a CRAM file

*.dict

Output

name:type
description
pattern

split_read_evidence{:bash}

meta{:bash}

:map

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

*.sr.txt.gz{:bash}

:file

Output file for split read evidence

*.sr.txt.gz

split_read_evidence_index{:bash}

meta{:bash}

:map

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

*.sr.txt.gz.tbi{:bash}

:file

Index of the output file for split read evidence

*.sr.txt.gz.tbi

paired_end_evidence{:bash}

meta{:bash}

:map

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

*.pe.txt.gz{:bash}

:file

Output file for paired end evidence

*.pe.txt.gz

paired_end_evidence_index{:bash}

meta{:bash}

:map

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

*.pe.txt.gz.tbi{:bash}

:file

Index of the output file for paired end evidence

*.pe.txt.gz.tbi

site_depths{:bash}

meta{:bash}

:map

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

*.sd.txt.gz{:bash}

:file

Output file for site depths

*.sd.txt.gz

site_depths_index{:bash}

meta{:bash}

:map

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

*.sd.txt.gz.tbi{:bash}

:file

Index of the output file for site depths

*.sd.txt.gz.tbi

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

maintainer
Github user nvnieuwk
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