From 91f4d9e4b7fd1586a9547fcaeb551159e04feed1 Mon Sep 17 00:00:00 2001
From: Leandro Lima <lelimaufc@gmail.com>
Date: Tue, 24 Mar 2020 08:45:58 -0300
Subject: [PATCH] Adding script with bash commands

---
 whole-genome-analysis/script.sh | 134 ++++++++++++++++++++++++++++++++
 1 file changed, 134 insertions(+)
 create mode 100644 whole-genome-analysis/script.sh

diff --git a/whole-genome-analysis/script.sh b/whole-genome-analysis/script.sh
new file mode 100644
index 0000000..4040dc9
--- /dev/null
+++ b/whole-genome-analysis/script.sh
@@ -0,0 +1,134 @@
+# analysis.sh
+# C: Jul  8, 2019
+# M: Feb 26, 2020
+# A: Leandro Lima <leandro.lima@gladstone.ucsf.edu>
+
+
+########################################
+## Variables with tools and databases ##
+########################################
+
+
+REF_GENOME=/root/resources/chr19.fa
+DATA_DIR=/root/data/
+GATK_DIR=/root/tools/GenomeAnalysisTK-3.8-1-0
+
+
+#############
+## Mapping ##
+#############
+
+
+cd /root/analysis
+
+
+# BWA - http://bio-bwa.sourceforge.net/bwa.shtml
+
+bwa mem $REF_GENOME $DATA_DIR/patient3.1.fastq.gz $DATA_DIR/patient3.2.fastq.gz > patient3.sam
+bwa mem $REF_GENOME $DATA_DIR/patient4.1.fastq.gz $DATA_DIR/patient4.2.fastq.gz > patient4.sam
+bwa mem $REF_GENOME $DATA_DIR/patient5.1.fastq.gz $DATA_DIR/patient5.2.fastq.gz > patient5.sam
+
+
+# Picard - https://broadinstitute.github.io/picard/command-line-overview.html#Overview
+
+# SAM to BAM, with read group information
+for pat_id in patient3 patient4 patient5; do
+    java -jar /root/tools/picard.jar AddOrReplaceReadGroups \
+          I=$pat_id.sam \
+          O=$pat_id.bam \
+          RGID=4 \
+          RGLB=lib1 \
+          RGPL=illumina \
+          RGPU=unit1 \
+          RGSM=$pat_id 
+done
+
+
+# Samtools - http://www.htslib.org/doc/samtools.html
+
+# Sort
+samtools sort patient3.bam -o patient3.sort.bam
+samtools sort patient4.bam -o patient4.sort.bam
+samtools sort patient5.bam -o patient5.sort.bam
+
+# Create index
+samtools index patient3.sort.bam
+samtools index patient4.sort.bam
+samtools index patient5.sort.bam
+
+
+
+# Check file sizes
+ls -lh
+
+# Remove SAM file
+
+# Check some flags (number of mapped/unmapped reads, etc.)
+
+
+#####################
+## Variant Calling ##
+#####################
+
+
+# GATK Haplotype Caller - https://gatk.broadinstitute.org/hc/en-us/articles/360037225632-HaplotypeCaller
+
+GATK_DIR=/root/tools/GenomeAnalysisTK-3.8-1-0
+
+for pat_id in patient3 patient4 patient5; do
+    java -jar $GATK_DIR/GenomeAnalysisTK.jar \
+        -T HaplotypeCaller \
+        -R $REF_GENOME \
+        -I $pat_id.sort.bam \
+        -o $pat_id.gatk.g.vcf \
+        --emitRefConfidence GVCF
+done
+
+
+# GATK Joint Genotyping
+java -jar $GATK_DIR/GenomeAnalysisTK.jar \
+    -T GenotypeGVCFs \
+    -R $REF_GENOME \
+    --variant patient3.gatk.g.vcf \
+    --variant patient4.gatk.g.vcf \
+    --variant patient5.gatk.g.vcf \
+    -o all_patients.vcf
+
+
+################
+## Annotation ##
+################
+
+
+# snpEff - http://snpeff.sourceforge.net/SnpEff_manual.html
+
+SNPEFF_DIR=/root/tools/snpEff
+# snpEff
+java -Xmx4g -jar $SNPEFF_DIR/snpEff.jar \
+    -v -stats all_patients.html \
+    GRCh38.86 all_patients.vcf > all_patients.ann.vcf
+
+# Adding ID field from dbSNP
+java -jar $SNPEFF_DIR/SnpSift.jar annotate \
+    -id /root/resources/dbSNP_chr19.vcf.gz \
+    all_patients.ann.vcf > all_patients.dbSnp.vcf
+
+rm all_patients.ann.vcf
+
+
+###################
+## APOE analysis ##
+###################
+
+
+# SnpSift extractFields - http://snpeff.sourceforge.net/SnpSift.html#Extract
+
+# Extracting gene name, rsID and genotypes
+cat all_patients.dbSnp.vcf | grep CHROM | cut -f1-5,8,10- > APOE_status.txt
+java -jar /root/tools/snpEff/SnpSift.jar \
+    extractFields \
+    all_patients.dbSnp.vcf \
+    CHROM POS ID REF ALT EFF[0].GENE GEN[*].GT \
+    | grep -E 'rs429358|rs7412' >> APOE_status.txt 
+
+column -t APOE_status.txt