Filter, sort and markdup sam/bam files, with optional BQSR and variant calling.
Input
name:type
description
pattern
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
bam:file
Input SAM/BAM file
*.{bam,sam}
bai:file
Input BAM file index
*.bai
target_regions_bed:file
Optional BED file containing target regions for BQSR and variant calling.
*.bed
filter_regions_bed:file
Optional BED file containing regions to filter.
*.bed
intermediate_bqsr_tables:file
Optional list of BQSR tables, used when parsing files created by elprep split
*.table
recall_file:file
Recall file with intermediate results for bqsr
*.recall
meta2:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
reference_sequences:file
Optional SAM header to replace existing header.
*.sam
meta3:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
reference_elfasta:file
Elfasta file, required for BQSR and variant calling.
*.elfasta
meta4:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
known_sites_elsites:file
Optional elsites file containing known SNPs for BQSR.
*.elsites
run_haplotypecaller:boolean
Run variant calling on the input files. Needed to generate gvcf output.
run_bqsr:boolean
Run BQSR on the input files. Needed to generate recall metrics.
bqsr_tables_only:boolean
Write intermediate BQSR tables, used when parsing files created by elprep split.
get_activity_profile:boolean
Get the activity profile calculated by the haplotypecaller to the given file in IGV format.
get_assembly_regions:boolean
Get the assembly regions calculated by haplotypecaller to the specified file in IGV format.
Output
name:type
description
pattern
bam
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.{bam,sam}
*.{bam,sam}:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.{bam,sam}
logs
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
elprep-*.log
*.log:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
elprep-*.log
metrics
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.{metrics.txt}
*.metrics.txt:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.{metrics.txt}
recall
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.{recall}
*.recall:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.{recall}
gvcf
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.{vcf.gz}
*.vcf.gz:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.{vcf.gz}
table
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.{table}
*.table:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.{table}
activity_profile
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.{activity_profile.igv}
*.activity_profile.igv:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.{activity_profile.igv}
assembly_regions
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.{assembly_regions.igv}
*.assembly_regions.igv:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.{assembly_regions.igv}
versions
versions.yml:file
File containing software versions
versions.yml
Tools
elprep
AGPL v3
elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4.
