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flagstats.sh
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flagstats.sh
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#!/bin/bash
##########################################################################
#
# Platform: NCI Gadi HPC
# Usage: this script is run by flagstats_run_parallel.pbs
# Version: 2.0
#
# For more details see: https://github.com/Sydney-Informatics-Hub/Fastq-to-BAM
#
# If you use this script towards a publication, please acknowledge the
# Sydney Informatics Hub (or co-authorship, where appropriate).
#
# Suggested acknowledgement:
# The authors acknowledge the support provided by the Sydney Informatics Hub,
# a Core Research Facility of the University of Sydney. This research/project
# was undertaken with the assistance of resources and services from the National
# Computational Infrastructure (NCI), which is supported by the Australian
# Government, and the Australian BioCommons which is enabled by NCRIS via
# Bioplatforms Australia funding.
#
##########################################################################
set -e
labSampleID=$1
bam=../Final_bams/${labSampleID}.final.bam
flags=../Final_bams/${labSampleID}.final.flagstats
samtools flagstat -@ $NCPUS -O tsv $bam > $flags