From a04a47a7ab78fe79a9dcc1c2834f2277cb6a1d56 Mon Sep 17 00:00:00 2001
From: user name <kdonnel2@sdf-cs1.eidf.epcc.ed.ac.uk>
Date: Tue, 12 Nov 2024 11:02:27 +0000
Subject: [PATCH] Added script to tests/scripts directory to test stochasticity
of bwa-mem
---
tests/scripts/bwa_stochasticity_check.sh | 45 ++++++++++++++++++++++++
1 file changed, 45 insertions(+)
create mode 100644 tests/scripts/bwa_stochasticity_check.sh
diff --git a/tests/scripts/bwa_stochasticity_check.sh b/tests/scripts/bwa_stochasticity_check.sh
new file mode 100644
index 0000000..441d29f
--- /dev/null
+++ b/tests/scripts/bwa_stochasticity_check.sh
@@ -0,0 +1,45 @@
+#!/bin/bash
+#SBATCH --cpus-per-task=16
+#SBATCH --mem=72GB
+#SBATCH --time=24:00:00
+#SBATCH --job-name=bwa_test
+#SBATCH --output=bwa_test.out
+#SBATCH --error=bwa_test.err
+
+BWA=/home/u035/u035/shared/software/bcbio/anaconda/bin/bwa
+SAMTOOLS=/home/u035/u035/shared/software/bcbio/anaconda/bin/samtools
+
+#Point to appropriate bwa index
+#In the pipeline, a softlink to this would be provided in the working directory
+INDEX=`find -L ./ -name "*.amb" | sed 's/\.amb$//'`
+
+#Run bwa on identical fastq input three times
+#These example input files are from 20240902_Ansari_Morad
+#We are picking them up from the pipeline immediately after outpu by fastp
+
+for i in $(seq 1 3)
+do
+$BWA mem \
+ -R '@RG\tID:158063\tPL:illumina\tPU:158063\tSM:158063' -c 250 -M \
+ -t 16 \
+ $INDEX \
+ subset_158063_1.fastq.gz subset_158063_2.fastq.gz \
+ | $SAMTOOLS view --threads 16 -o "${i}_158063_.bam" -
+done
+
+#We expect the headers to differ
+#To be confident, let's compare headerless sam
+for i in $(seq 1 3)
+do
+$SAMTOOLS view "${i}_158063_.bam" > "${i}_158063_.sam"
+done
+
+#Finally, generate md5 checksums for each sam
+#These should be identical
+for i in $(seq 1 3)
+do
+md5sum "${i}_158063_.sam" > "${i}_158063_.sam.md5"
+done
+
+
+
--
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