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}

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 (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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

bam (file)

Sorted, markdup, optionally BQSR BAM/SAM file

*.{bam,sam}

metrics (file)

Optional duplicate metrics file generated by elprep

*.{metrics.txt}

recall (file)

Optional recall metrics file generated by elprep

*.{recall}

gvcf (file)

Optional GVCF output file

*.{vcf.gz}

table (file)

Optional intermediate BQSR table output file

*.{table}

activity_profile (file)

Optional activity profile output file

*.{activity_profile.igv}

assembly_regions (file)

Optional activity regions output file

*.{assembly_regions.igv}
maintainer
Github user matthdsm
get in touch
Ask a question on Slack Open an issue on GitHub

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.

github.com/ExaScience/elprep 10.1371/journal.pone.0244471