#!/usr/bin/env bash

CIS_X_HOME=$(realpath $(dirname $0)/../../..)
CIS_X_CORE_HOME=$(realpath $(dirname $0)/..)

SAMPLE_ID=$1
HIGH20=$2
CNVLOH=$3
SNV4_OUT=$4
HET_OUT=$5
COVG_WGS=$6

BADLST=$CIS_X_HOME/refs/SuperBad.good.bad.new

perl $CIS_X_CORE_HOME/src/01.get.markder.pl \
    $SAMPLE_ID \
    $HIGH20 \
    $CNVLOH \
    $SNV4_OUT \
    $HET_OUT \
    $BADLST \
    $COVG_WGS
