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}
:file
BAM/SAM file
*.{bam,sam}
logs
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.log
:file
Log file
elprep-*.log
metrics
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.metrics.txt
:file
Metrics file
*.{metrics.txt}
recall
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.recall
:file
Recall file
*.{recall}
gvcf
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.vcf.gz
:file
VCF file
*.{vcf.gz}
table
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.table
:file
Table
*.{table}
activity_profile
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.activity_profile.igv
:file
Activity profile
*.{activity_profile.igv}
assembly_regions
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.assembly_regions.igv
:file
Assembly regions
*.{assembly_regions.igv}
versions_elprep
${task.process}
:string
The name of the process
elprep
:string
The name of the tool
elprep 2>&1 | sed -n '2s/^.*version //;s/ compiled.*$//p'
:eval
The expression to obtain the version of the tool
Topics
name:type
description
pattern
versions
${task.process}
:string
The name of the process
elprep
:string
The name of the tool
elprep 2>&1 | sed -n '2s/^.*version //;s/ compiled.*$//p'
:eval
The expression to obtain the version of the tool
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.
