From d7d436c2fa104d29570bad1668b4105ce71f2ec9 Mon Sep 17 00:00:00 2001
From: Laura Cook <l.cook2@student.unimelb.edu.au>
Date: Fri, 11 Sep 2020 12:14:24 +1000
Subject: [PATCH] first commit. script to subsample BAM files in a directory
---
dunnart/scripts/subsample.sh | 17 +++++++++++++++++
1 file changed, 17 insertions(+)
create mode 100644 dunnart/scripts/subsample.sh
diff --git a/dunnart/scripts/subsample.sh b/dunnart/scripts/subsample.sh
new file mode 100644
index 0000000..322a400
--- /dev/null
+++ b/dunnart/scripts/subsample.sh
@@ -0,0 +1,17 @@
+
+
+TRA=($(for file in B*_PPq30.sorted.dedup.bam; do echo $file |cut -d "_" -f 1-2;done))
+
+echo ${TRA[@]}
+
+for tr in ${TRA[@]};
+
+do
+
+echo ${tr}
+
+frac=$( samtools idxstats ${tr}_PPq30.sorted.dedup.bam | cut -f3 | awk 'BEGIN {total=0} {total += $1} END {frac=10000000/total; if (frac > 1) {print 1} else {print frac}}' )
+
+samtools view -bs $frac ${tr}_PPq30.sorted.dedup.bam > ../../results_10M/bowtie2/${tr}_PPq30.sorted.dedup.bam
+
+done
--
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