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 (map)

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

]

input (file)

BAM/CRAM/SAM file

*.{bam,cram,sam}

input_index (file)

Index of the BAM/CRAM/SAM file

*.{bai,crai,sai}

site_depth_vcf (file)

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

*.vcf.gz

site_depth_vcf_index (file)

Optional - index of the VCF file, needed for the site depths output

*.tbi

fasta (file)

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

*.{fasta,fa}

fasta_fai (file)

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

*.fai

dict (file)

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

*.dict

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

split_read_evidence (file)

Output file for split read evidence

*.sr.txt.gz

split_read_evidence_index (file)

Index of the output file for split read evidence

*.sr.txt.gz.tbi

paired_end_evidence (file)

Output file for paired end evidence

*.pe.txt.gz

paired_end_evidence_index (file)

Index of the output file for paired end evidence

*.pe.txt.gz.tbi

site_depths (file)

Output file for site depths

*.sd.txt.gz

site_depths_index (file)

Index of the output file for site depths

*.sd.txt.gz.tbi
author
Github user nvnieuwk
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