Description

Filter, sort and markdup sam/bam files, with optional BQSR and variant calling.

Input

Name
Description
Pattern

0 ()

1 ()

2 ()

3 ()

4 ()

5 ()

6 ()

0 ()

1 ()

0 ()

1 ()

0 ()

1 ()

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
Description
Pattern

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

Tools

elprep Documentation

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.

doi: 10.1371/journal.pone.0244471License: AGPL v3
Authors