From 8f424cd196951acc55799706869f22c2a118629f Mon Sep 17 00:00:00 2001 From: RoanKanninga Date: Mon, 12 Nov 2018 13:30:28 +0100 Subject: [PATCH] bugfixes in prepare_NGS_bedfiles --- prepare_NGS_Bedfiles.sh | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/prepare_NGS_Bedfiles.sh b/prepare_NGS_Bedfiles.sh index 587101d..149a7f9 100755 --- a/prepare_NGS_Bedfiles.sh +++ b/prepare_NGS_Bedfiles.sh @@ -206,6 +206,7 @@ then sort -V -k1 -k2 -k3 "${TMP}/${NAME}.per_base.intervals" | uniq > "${baits}.uniq.per_base.intervals.tmp" head -n 86 "${baits}.interval_list" > "${baits}.uniq.per_base.interval_list" sort -V "${baits}.uniq.per_base.intervals.tmp" >> "${baits}.uniq.per_base.interval_list" + tail -n+87 "${baits}.uniq.per_base.interval_list" | awk '{print $1"\t"$2"\t"($3+1)"\t"$5}' > "${baits}.uniq.per_base.bed" fi fi @@ -323,7 +324,7 @@ else BATCH_ALL=$((BATCHCOUNT + batchCount_X)) #move the X chromosome folders lengthR=$(less "${phiXRef}" | wc -l) - lengthRef=$(( "${lengthR}" + 2 )) + lengthRef=$(( ${lengthR} + 2 )) if [ "${lengthOFChrXNP1}" -ne "${lengthOFChrXNP2}" ] then for i in $(seq 1 ${batchCount_X}) @@ -455,3 +456,4 @@ fi bedtools intersect -a ${baits}.merged.bed -b /apps/data/GSAarray/GSA_sorted.bed | uniq > GSA_SNPS.bed +