HG002_small_variant_calling_test_run.md

Preparing the output of Guppy and Minimap2 to test PEPPER-Margin-DeepVariant pipeline for a subset of chromosomes for HG002

• Set up the host instance using these instructions
• Create a working directory

WORK_DIR=/data/hg002_pmdv
mkdir -p $WORK_DIR/

• Create the configuration file (e.g. sample.config in the $PROJECT_DIR)

cp $PROJECT_DIR/sample.config $WORK_DIR/
CONFIG_PATH=$WORK_DIR/sample.config

• Create a Google Storage Bucket with a unique name and add the configuration file to it e.g.

BUCKET=gs://urwgs_hg002_test_$(date +%s)
gsutil mb $BUCKET
sed -i "s|^BUCKET=.*$|BUCKET=${BUCKET}|g" $CONFIG_PATH
gsutil cp $CONFIG_PATH ${BUCKET}/sample.config

• Transfer data and create the appropriate directory for testing

$PROJECT_DIR/simulation/simulate_alignment_output.sh

• Add cron job for deleting instances based on the status from the instances

(crontab -u $USER -l; echo -e "*/3 * * * * bash -c $PROJECT_DIR/manage_instances/delete_instances_pmdv_wrapper.sh >> /data/logs/delete_instances_stdout.log 2>> /data/logs/delete_instances_stderr.log") | crontab -u $USER - 

• Start 2 instances to run PEPPER-Margin-DeepVariant on chr2 and chr16,chr21

parallel -j 2 $PROJECT_DIR/manage_instances/pmdv_instance.sh ::: \
	pmdv-{1..2} :::+ \
	chr2 \
	chr16:chr21 ::: \
	${BUCKET}/sample.config

• The generated output is transferred to $BUCKET/pmdv_${DV}_${DV_MODEL}_output.