<commit_before>#!/bin/bash
#set -xe
set -xeuo pipefail

usage="USAGE:
bash 04-filter_qsub.sh <sample_list.txt> <genome.fa> <CalculateHsMetrics_reference.bed> <intersect_regions.bed>
for example:
bash \
/home/springer/pcrisp/gitrepos/springerlab_methylation/SeqCap/04-filter_qsub.sh \
single_sample.txt \
/home/springer/pcrisp/ws/refseqs/maize/Zea_mays.AGPv4.dna.toplevel.fa \
/home/springer/pcrisp/ws/refseqs/maize/seqcapv2_onTarget-for-picard.bed
"

#define stepo in the pipeline - should be the same name as the script
step=04-filter

######### Setup ################
sample_list=$1
genome_reference=$2
CalculateHsMetrics_reference=$3
<commit_msg>comments edited<commit_after>#!/bin/bash
#set -xe
set -xeuo pipefail

usage="USAGE:
bash 04-filter_qsub.sh <sample_list.txt> <genome.fa> <CalculateHsMetrics_reference.bed>
for example:
bash \
/home/springer/pcrisp/gitrepos/springerlab_methylation/SeqCap/04-filter_qsub.sh \
single_sample.txt \
/home/springer/pcrisp/ws/refseqs/maize/Zea_mays.AGPv4.dna.toplevel.fa \
/home/springer/pcrisp/ws/refseqs/maize/seqcapv2_onTarget-for-picard.bed
"

#define stepo in the pipeline - should be the same name as the script
step=04-filter

######### Setup ################
sample_list=$1
genome_reference=$2
CalculateHsMetrics_reference=$3

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