From 683f81a9262df3842a7c20e6df8a31c02091cdad Mon Sep 17 00:00:00 2001
From: gwc32007 <43821509+gwc32007@users.noreply.github.com>
Date: Tue, 19 Feb 2019 11:27:47 -0500
Subject: [PATCH] Create UKP8_SNPAnalysis

---
 UKP8_SNPAnalysis | 127 +++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 127 insertions(+)
 create mode 100644 UKP8_SNPAnalysis

diff --git a/UKP8_SNPAnalysis b/UKP8_SNPAnalysis
new file mode 100644
index 0000000..77e3091
--- /dev/null
+++ b/UKP8_SNPAnalysis
@@ -0,0 +1,127 @@
+#indexes reference genome
+
+#PBS -S /bin/bash
+#PBS -N j_bwa
+#PBS -l walltime=128:00:00
+#PBS -l nodes=1:ppn=1:AMD
+#PBS -q batch
+
+cd $PBS_O_WORKDIR
+
+module load BWA/0.7.17-foss-2016b
+time bwa index /scratch/gwc32007/crypto_genomes/cparvum_iowaII_genome.fasta
+
+#aligns reads to reference genome
+
+#PBS -S /bin/bash
+#PBS -N j_bwa
+#PBS -l walltime=128:00:00
+#PBS -l nodes=1:ppn=1:AMD
+#PBS -q batch
+
+cd $PBS_O_WORKDIR
+
+module load BWA/0.7.17-foss-2016b
+time bwa mem -M -t 16 /scratch/gwc32007/crypto_genomes/cparvum_iowaII_genome.fasta /scratch/gwc32007/crypto_fastq/UKP8/SRR6148259_1.fastq.gz /scratch/gwc32007/crypto_fastq/UKP8/SRR6148259_2.fastq.gz > /scratch/gwc32007/fastq_alignments/UKP8_aln.sam
+
+#converts the .sam file to a more condensed .bam file
+
+#PBS -S /bin/bash
+#PBS -N j_s_samtools
+#PBS -q batch
+#PBS -l nodes=1:ppn=1:AMD
+#PBS -l mem=100gb
+#PBS -l walltime=480:00:00
+
+cd $PBS_O_WORKDIR
+
+module load SAMtools/1.6-foss-2016b
+time samtools view -bt /scratch/gwc32007/crypto_genomes/cparvum_iowaII_genome.fasta -o /scratch/gwc32007/fastq_alignments/UKP8_aln.bam /scratch/gwc32007/fastq_alignments/UKP8_aln.sam
+
+#sorts the alignments from smallest to largest
+
+#PBS -S /bin/bash
+#PBS -N j_s_samtools
+#PBS -q batch
+#PBS -l nodes=1:ppn=1:AMD
+#PBS -l mem=100gb
+#PBS -l walltime=480:00:00
+
+cd $PBS_O_WORKDIR
+
+module load SAMtools/1.6-foss-2016b
+
+time samtools sort /scratch/gwc32007/fastq_alignments/UKP8_aln.bam -o /scratch/gwc32007/fastq_alignments/UKP8_aln.sorted.bam
+
+#marks the duplicate reads in the alignment
+
+#PBS -S /bin/bash
+#PBS -N j_picard
+#PBS -q batch
+#PBS -l nodes=1:ppn=1:AMD
+#PBS -l walltime=480:00:00
+#PBS -l mem=25g
+
+cd $PBS_O_WORKDIR
+
+module load picard/2.16.0-Java-1.8.0_144
+time java -Xmx20g -classpath "/usr/local/apps/eb/picard/2.16.0-Java-1.8.0_144" -jar  /usr/local/apps/eb/picard/2.16.0-Java-1.8.0_144/picard.jar MarkDuplicates I=/scratch/gwc32007/fastq_alignments/UKP8_aln.sorted.bam O=/scratch/gwc32007/fastq_alignments/UKP8_aln.sorted_duplicates.bam M=marked_dup_metrics.txt REMOVE_DUPLICATES=false
+
+#replaces read groups in the bam file with one read group
+
+#PBS -S /bin/bash
+#PBS -N j_picard
+#PBS -q batch
+#PBS -l nodes=1:ppn=1:AMD
+#PBS -l walltime=480:00:00
+#PBS -l mem=25g
+
+cd $PBS_O_WORKDIR
+
+module load picard/2.16.0-Java-1.8.0_144
+time java -Xmx20g -classpath "/usr/local/apps/eb/picard/2.16.0-Java-1.8.0_144" -jar  /usr/local/apps/eb/picard/2.16.0-Java-1.8.0_144/picard.jar AddOrReplaceReadGroups I=/scratch/gwc32007/fastq_alignments/UKP8_aln.sorted_duplicates.bam O=/scratch/gwc32007/fastq_alignments/UKP8_aln.dupl.read.sort.bam SORT_ORDER=coordinate RGLB=lib1 RGPL=illumina RGSM=20 RGPU=unit1 VALIDATION_STRINGENCY=LENIENT 
+
+#indexing the reference
+
+#PBS -S /bin/bash
+#PBS -N j_s_samtools
+#PBS -q batch
+#PBS -l nodes=1:ppn=1:AMD
+#PBS -l mem=100gb
+#PBS -l walltime=480:00:00
+
+cd $PBS_O_WORKDIR
+
+module load SAMtools/1.6-foss-2016b
+
+time samtools faidx /scratch/gwc32007/crypto_genomes/cparvum_iowaII_genome.fasta
+
+time samtools index /scratch/gwc32007/fastq_alignments/UKP8_aln.dupl.read.sort.bam
+
+#creating dictionary for reference
+
+module load picard/2.16.0-Java-1.8.0_144
+#PBS -S /bin/bash
+#PBS -N j_picard
+#PBS -q batch
+#PBS -l nodes=1:ppn=1:AMD
+#PBS -l walltime=480:00:00
+#PBS -l mem=25g
+
+cd $PBS_O_WORKDIR
+
+module load picard/2.16.0-Java-1.8.0_144
+time java -Xmx20g -classpath "/usr/local/apps/eb/picard/2.16.0-Java-1.8.0_144" -jar  /usr/local/apps/eb/picard/2.16.0-Java-1.8.0_144/picard.jar CreateSequenceDictionary R=/scratch/gwc32007/crypto_genomes/cparvum_iowaII_genome.fasta O=/scratch/gwc32007/crypto_genomes/cparvum_iowaII_genome.dict
+
+#find SNP calls in the alignments
+
+#PBS -S /bin/bash
+#PBS -N j_gatk
+#PBS -q batch
+#PBS -l nodes=1:ppn=1
+#PBS -l walltime=48:00:00
+#PBS -l mem=2gb
+
+module load GATK/3.8-0-Java-1.8.0_144
+
+java -Xmx4g -jar /usr/local/apps/eb/GATK/3.8-0-Java-1.8.0_144/GenomeAnalysisTK.jar -T HaplotypeCaller -R /scratch/gwc32007/crypto_genomes/cparvum_iowaII_genome.fasta -I /scratch/gwc32007/fastq_alignments/UKP8_aln.dupl.read.sort.bam -o /scratch/gwc32007/SNPGenie/gvcf_CURO/UKP8_output.g.vcf.gz -ERC GVCF