Description

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}

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

]

reference_sequences:file

Optional SAM header to replace existing header.

*.sam

meta3:map

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

]

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

]

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 speficied file in IGV format.

Output

name:type
description
pattern

bam

meta:map

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

]

*.{bam,sam}

*.{bam,sam}:map

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

]

*.{bam,sam}

logs

meta:map

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

]

elprep-*.log

*.log:map

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

]

elprep-*.log

metrics

meta:map

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

]

*.{metrics.txt}

*.metrics.txt:map

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

]

*.{metrics.txt}

recall

meta:map

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

]

*.{recall}

*.recall:map

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

]

*.{recall}

gvcf

meta:map

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

]

*.{vcf.gz}

*.vcf.gz:map

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

]

*.{vcf.gz}

table

meta:map

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

]

*.{table}

*.table:map

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

]

*.{table}

activity_profile

meta:map

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

]

*.{activity_profile.igv}

*.activity_profile.igv:map

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

]

*.{activity_profile.igv}

assembly_regions

meta:map

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

]

*.{assembly_regions.igv}

*.assembly_regions.igv:map

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

]

*.{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.