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Treat no BED file as a WGS, create WGS bed #10

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Treat no BED file as a WGS, create WGS bed #10

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7 changes: 6 additions & 1 deletion segments/qc-target-reads-gatk.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -91,7 +91,12 @@ fi

found_bed=$(find "$proj_dir" -maxdepth 1 -type f -iname "*.bed" | grep -v "probes" | sort | head -1)
bed=$(bash "${code_dir}/scripts/get-set-setting.sh" "${proj_dir}/settings.txt" EXP-TARGETS-BED "$found_bed");

# Chek if there is no bed file in the project directory, treat as WGS and create a bed for all chromosome ranges
if [ ! -s "$bed" ] ; then
awk 'OFS="\t"{print $1, "0", $2}' ${ref_fasta}.fai > ${proj_dir}/wgs.bed
found_bed=$(find "$proj_dir" -maxdepth 1 -type f -iname "*.bed" | grep -v "probes" | sort | head -1)
bed=$(bash "${code_dir}/scripts/get-set-setting.sh" "${proj_dir}/settings.txt" EXP-TARGETS-BED "$found_bed");
fi
if [ ! -s "$bed" ] ; then
echo -e "\n $script_name ERROR: BED $bed DOES NOT EXIST \n" >&2
exit 1
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