PacBio WGS Variant Pipeline performs read alignment, variant calling, and phasing. Joint-calling of small variants and structural variants for cohorts and optional variant filtering and annotation is also available for HiFi human WGS.

• GitHub Repository

• Module Name: hifi-human-wgs (see the modules page for more information)
• Environment variables set
• HIFIHUMANWGS_HOME
• Template inputs configuration file in $HIFIHUMANWGS_HOME/inputs.json
• Test data in $HIFIHUMANWGS_HOME/test
• Reference data in /fdb/hifi-human-wgs

This application on biowulf has only been tested with miniwdl, not cromwell. Furthermore, only the single-node run mode option is supported currently, due to incompatibility of miniwdl-slurm with the Biowulf configuration.

To run this workflow, you will need to prepare an inputs.json file. You can use $HIFIHUMANWGS_HOME/inputs.json as a template. Here, we will be using an example consisting of a toy Revio HiFi dataset. The inputs file for this is prepared in $HIFIHUMANWGS_HOME/test/small_revio_inputs.json.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --mem 64g -c32 
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load hifi-human-wgs

[user@cn3144 ~]$ miniwdl run $HIFIHUMANWGS_HOME/workflows/main.wdl -i $HIFIHUMANWGS_HOME/test/small_revio_inputs.json

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. hifi-human-wgs.sh). For example:

#!/bin/bash
set -e
module load hifi-human-wgs
miniwdl run $HIFIHUMANWGS_HOME/workflows/main.wdl -i $HIFIHUMANWGS_HOME/test/small_revio_inputs.json

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] hifi-human-wgs.sh