Create bqsr_recal_nonhuman.sh

bqsr_recal_nonhuman.sh

@@ -0,0 +1,56 @@
+#!/bin/bash
+
+##########################################################################
+#
+# Platform: NCI Gadi HPC
+# Usage: this script is run by bqsr_recal_run_parallel.pbs
+# Version: 2.0
+#
+# For more details see: https://github.com/Sydney-Informatics-Hub/Fastq-to-BAM
+#
+# If you use this script towards a publication, please acknowledge the
+# Sydney Informatics Hub (or co-authorship, where appropriate).
+#
+# Suggested acknowledgement:
+# The authors acknowledge the support provided by the Sydney Informatics Hub,
+# a Core Research Facility of the University of Sydney. This research/project
+# was undertaken with the assistance of resources and services from the National
+# Computational Infrastructure (NCI), which is supported by the Australian
+# Government, and the Australian BioCommons which is enabled by NCRIS via
+# Bioplatforms Australia funding.
+#
+##########################################################################
+
+
+labSampleID=`echo $1 | cut -d ',' -f 1`
+intNum=`echo $1 | cut -d ',' -f 2`
+interval=`echo $1 | cut -d ',' -f 3`
+
+echo $labSampleID $intNum $interval
+
+bam=../Dedup_sort/${labSampleID}.coordSorted.dedup.bam
+log=./Logs/BQSR_recal/${labSampleID}.${intNum}.log
+err=./Logs/BQSR_recal_error_capture/${labSampleID}.${intNum}.err
+out=../BQSR_tables/${labSampleID}.${intNum}.recal_data.table
+
+ref=
+dbsnp= # edit this depending on your reference
+
+gatk BaseRecalibrator \
+        --java-options "-Xmx20g -DGATK_STACKTRACE_ON_USER_EXCEPTION=true" \
+        -R $ref \
+        -L $interval \
+        -I $bam  \
+        --known-sites $dbsnp \
+        -O $out >> $log 2>&1
+
+
+if grep -q -i error $log
+then
+        printf "Error in GATK log ${log}\n" >> $err
+fi
+
+if grep -q Exception $log
+then
+        printf "Exception in GATK log ${log}\n" >> $err
+fi