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
]
bam:file
Input SAM/BAM file
*.{bam,sam}
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.
reference_sequences:file
Optional SAM header to replace existing header.
*.sam
filter_regions_bed:file
Optional BED file containing regions to filter.
*.bed
reference_elfasta:file
Elfasta file, required for BQSR and variant calling.
*.elfasta
known_sites_elsites:file
Optional elsites file containing known SNPs for BQSR.
*.elsites
target_regions_bed:file
Optional BED file containing target regions for BQSR and variant calling.
*.bed
intermediate_bqsr_tables:file
Optional list of BQSR tables, used when parsing files created by elprep split
*.table
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 speficied file in IGV format.
Output
name:type
description
pattern
bam
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
output/**.{bam,sam}:file
Sorted, markdup, optionally BQSR BAM/SAM file
*.{bam,sam}
logs
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
logs/elprep/elprep*:list
Runtime log files
elprep-*.log
metrics
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.metrics.txt:file
Optional duplicate metrics file generated by elprep
*.{metrics.txt}
recall
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.recall:file
Optional recall metrics file generated by elprep
*.{recall}
gvcf
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.vcf.gz:file
Optional GVCF output file
*.{vcf.gz}
table
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.table:file
Optional intermediate BQSR table output file
*.{table}
activity_profile
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.activity_profile.igv:file
Optional activity profile output file
*.{activity_profile.igv}
assembly_regions
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.assembly_regions.igv:file
Optional activity regions output file
*.{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.
