phase.ukb

#!/bin/bash

set -e -o pipefail

if [ $# -ne 2 ]; then
  echo "usage: $0 PROJECT CHROM"
  exit
fi

project=$1
chrom=$2

size="200k"

filter='FILTER="PASS"&INFO/AAScore[*]>0.95&F_MISSING<0.05&TYPE="snp"'
# filter='FILTER="PASS"&INFO/AAScore[*]>0.95&F_MISSING<0.05'

# beagle_mem="340G"; beagle_instance_type="mem2_ssd1_v2_x96"; beagle_args="window=30"
# beagle_mem="460G"; beagle_instance_type="mem3_ssd1_v2_x64"; beagle_args=""
beagle_mem="700G"; beagle_instance_type="mem3_ssd1_v2_x96"; beagle_args=""

dx run ${project}:/apps/phase-ukb-${size} \
  -y \
  --name "phase-ukb-${size}.chr${chrom}" \
  --priority high \
  -i "project=${project}" \
  -i "chrom=${chrom}" \
  -i "filter=${filter}" \
  -i "beagle_instance_type=${beagle_instance_type}" \
  -i "beagle_mem=${beagle_mem}" \
  -i "beagle_args=${beagle_args}"