collect_insert_size_metrics.sh

#!/bin/bash

set -e

if [ "$#" -ne 4 ]; then
    echo "Usage: $0 <BAM_INPUT_PATH> <JOBLIST_FQ_FPATH_FNAME> <PICARD_JAR_FPATH> <OUTPUT_BASE_PATH>"
    exit 1
fi

# INPUT PATHS
BAM_INPUT_PATH=$1
JOBLIST_FQ_FPATH_FNAME=$2
PICARD_JAR_FPATH=$3

# OUTPUT PATHS
MARK_DUPLICATES_OUTPUT_PATH="$4/mark_duplicate_output"
COLLECT_INSERT_SIZES_OUTPUT_PATH="$4/collect_insert_metrics_output"

mkdir -p $COLLECT_INSERT_SIZES_OUTPUT_PATH

# LOG_PATHS
COLLECT_INSERT_SIZES_LOG_PATH=${COLLECT_INSERT_SIZES_OUTPUT_PATH}'/log'

mkdir -p $COLLECT_INSERT_SIZES_LOG_PATH

for LIBR_NAME in `cat ${JOBLIST_FQ_FPATH_FNAME}`
do
    echo `date '+%F %H:%M:%S'` ${LIBR_NAME} Running Mark Duplicates ...
    COMMAND="java -jar $PICARD_JAR_FPATH CollectInsertSizeMetrics INPUT=${MARK_DUPLICATES_OUTPUT_PATH}/${LIBR_NAME}_marked_duplicates.bam OUTPUT=${COLLECT_INSERT_SIZES_OUTPUT_PATH}/${LIBR_NAME}_insert_size_metric.tsv H=${COLLECT_INSERT_SIZES_OUTPUT_PATH}/${LIBR_NAME}_insert_size_metric.pdf" >> "${COLLECT_INSERT_SIZES_LOG_PATH}/${LIBR_NAME}_collect_insert_metrics_step.log"
    echo $COMMAND
    eval $COMMAND
    echo `date '+%F %H:%M:%S'` ${LIBR_NAME} Mark Duplicates completed.
    echo " "
    echo " "
done