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15-annotation.sh
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15-annotation.sh
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#!/bin/bash
export VCF_PATH=$HOME_PATH/vcf
DBSNP_FILE=$RESOURCES_PATH/dbSNP/dbSNP151.vcf.gz
DBNSFP_FILE=$RESOURCES_PATH/dbNSFP/dbNSFP2.9.3.txt.gz
GNOMAD_FILE=$RESOURCES_PATH/gnomAD/gnomad.exomes.r2.1.1.sites.vcf.bgz
if [ ! -d $SNPEFF_PATH/data ]
then
java -jar $SNPEFF_PATH/snpEff.jar download GRCh37.75
fi
## Haplotype Caller
# Variant effect annotation
java -Xmx4096m -jar $SNPEFF_PATH/snpEff.jar ann \
-v -noLog -noStats -noLof GRCh37.75 \
$VCF_PATH/haplotypecaller_filtered_norm.vcf.gz > $VCF_PATH/haplotypecaller_filtered_norm_eff.vcf
$HTSLIB_PATH/bgzip $VCF_PATH/haplotypecaller_filtered_norm_eff.vcf
$HTSLIB_PATH/tabix $VCF_PATH/haplotypecaller_filtered_norm_eff.vcf.gz
# Annotation with dbSNP
java -Xmx4096m -jar $SNPEFF_PATH/SnpSift.jar annotate \
-v -id $DBSNP_FILE \
$VCF_PATH/haplotypecaller_filtered_norm_eff.vcf.gz > $VCF_PATH/haplotypecaller_filtered_norm_eff_dbsnp.vcf
$HTSLIB_PATH/bgzip
$VCF_PATH/haplotypecaller_filtered_norm_eff_dbsnp.vcf.gz
$HTSLIB_PATH/tabix $VCF_PATH/haplotypecaller_filtered_norm_eff_dbsnp.vcf.gz
# Annotation with dbNSFP
java -Xmx4096m -jar $SNPEFF_PATH/SnpSift.jar dbnsfp \
-v -m -db $DBNSFP_FILE \
$VCF_PATH/haplotypecaller_filtered_norm_eff_dbsnp.vcf.gz > $VCF_PATH/haplotypecaller_filtered_norm_eff_dbsnp_dbnsfp.vcf
$HTSLIB_PATH/bgzip $VCF_PATH/haplotypecaller_filtered_norm_eff_dbsnp_dbnsfp.vcf
$HTSLIB_PATH/tabix $VCF_PATH/haplotypecaller_filtered_norm_eff_dbsnp_dbnsfp.vcf.gz
# Annotation with gnomAD
java -Xmx4096m -jar $SNPEFF_PATH/SnpSift.jar annotate \
-v $GNOMAD_FILE \
$VCF_PATH/haplotypecaller_filtered_norm_eff_dbsnp_dbnsfp.vcf.gz > $VCF_PATH/haplotypecaller_filtered_norm_eff_dbsnp_dbnsfp_gnomad.vcf
$HTSLIB_PATH/bgzip $VCF_PATH/haplotypecaller_filtered_norm_eff_dbsnp_dbnsfp_gnomad.vcf
$HTSLIB_PATH/tabix $VCF_PATH/haplotypecaller_filtered_norm_eff_dbsnp_dbnsfp_gnomad.vcf.gz
# FreeBayes
# Variant effect annotation
java -Xmx4096m -jar $SNPEFF_PATH/snpEff.jar ann \
-v -noLog -noStats -noLof GRCh37.75 \
$VCF_PATH/freebayes_filtered_norm.vcf.gz > $VCF_PATH/freebayes_filtered_norm_eff.vcf
$HTSLIB_PATH/bgzip $VCF_PATH/freebayes_filtered_norm_eff.vcf
$HTSLIB_PATH/tabix \
$VCF_PATH/freebayes_filtered_norm_eff.vcf.gz
# Annotation with dbSNP
java -Xmx4096m -jar $SNPEFF_PATH/SnpSift.jar annotate \
-v -id $DBSNP_FILE \
$VCF_PATH/freebayes_filtered_norm_eff.vcf.gz > $VCF_PATH/freebayes_filtered_norm_eff_dbsnp.vcf
$HTSLIB_PATH/bgzip\
$VCF_PATH/freebayes_filtered_norm_eff_dbsnp.vcf.gz
$HTSLIB_PATH/tabix \
$VCF_PATH/freebayes_filtered_norm_eff_dbsnp.vcf.gz
# Annotation with dbNSFP
java -Xmx4096m -jar $SNPEFF_PATH/SnpSift.jar dbnsfp \
-v -m -db $DBNSFP_FILE \
$VCF_PATH/freebayes_filtered_norm_eff_dbsnp.vcf.gz > $VCF_PATH/freebayes_filtered_norm_eff_dbsnp_dbnsfp.vcf
$HTSLIB_PATH/bgzip\
$VCF_PATH/freebayes_filtered_norm_eff_dbsnp_dbnsfp.vcf \
$HTSLIB_PATH/tabix \
$VCF_PATH/freebayes_filtered_norm_eff_dbsnp_dbnsfp.vcf.gz
# Annotation with gnomAD
java -Xmx4096m -jar $SNPEFF_PATH/SnpSift.jar annotate \
-v $GNOMAD_FILE \
$VCF_PATH/freebayes_filtered_norm_eff_dbsnp_dbnsfp.vcf.gz > $VCF_PATH/freebayes_filtered_norm_eff_dbsnp_dbnsfp_gnomad.vcf
$HTSLIB_PATH/bgzip\
$VCF_PATH/freebayes_filtered_norm_eff_dbsnp_dbnsfp_gnomad.vcf
$HTSLIB_PATH/tabix \
$VCF_PATH/freebayes_filtered_norm_eff_dbsnp_dbnsfp_gnomad.vcf.gz
## Deep Variant
# Variant effect annotation
java -Xmx4096m -jar $SNPEFF_PATH/snpEff.jar ann \
-v -noLog -noStats -noLof GRCh37.75 \
$VCF_PATH/deepvariant_filtered_norm.vcf.gz > $VCF_PATH/deepvariant_filtered_norm_eff.vcf.gz
$HTSLIB_PATH/bgzip \
$VCF_PATH/deepvariant_filtered_norm_eff.vcf
$HTSLIB_PATH/tabix \
$VCF_PATH/deepvariant_filtered_norm_eff.vcf.gz
# Annotation with dbSNP
java -Xmx4096m -jar $SNPEFF_PATH/SnpSift.jar annotate \
-v -id $DBSNP_FILE \
$VCF_PATH/deepvariant_filtered_norm_eff.vcf.gz > $VCF_PATH/deepvariant_filtered_norm_eff_dbsnp.vcf
$HTSLIB_PATH/bgzip\
$VCF_PATH/deepvariant_filtered_norm_eff_dbsnp.vcf
$HTSLIB_PATH/tabix \
$VCF_PATH/deepvariant_filtered_norm_eff_dbsnp.vcf.gz
# Annotation with dbNSFP
java -Xmx4096m -jar $SNPEFF_PATH/SnpSift.jar dbnsfp \
-v -m -db $DBNSFP_FILE \
$VCF_PATH/deepvariant_filtered_norm_eff_dbsnp.vcf.gz > $VCF_PATH/deepvariant_filtered_norm_eff_dbsnp_dbnsfp.vcf
$HTSLIB_PATH/bgzip\
$VCF_PATH/deepvariant_filtered_norm_eff_dbsnp_dbnsfp.vcf.gz
$HTSLIB_PATH/tabix \
$VCF_PATH/deepvariant_filtered_norm_eff_dbsnp_dbnsfp.vcf.gz
# Annotation with gnomAD
java -Xmx4096m -jar $SNPEFF_PATH/SnpSift.jar annotate \
-v $GNOMAD_FILE \
$VCF_PATH/deepvariant_filtered_norm_eff_dbsnp_dbnsfp.vcf.gz > $VCF_PATH/deepvariant_filtered_norm_eff_dbsnp_dbnsfp_gnomad.vcf.gz
$HTSLIB_PATH/bgzip\
$VCF_PATH/deepvariant_filtered_norm_eff_dbsnp_dbnsfp_gnomad.vcf
$HTSLIB_PATH/tabix \
$VCF_PATH/deepvariant_filtered_norm_eff_dbsnp_dbnsfp_gnomad.vcf.gz
# Remove intermediate files
rm $VCF_PATH/haplotypecaller_filtered_norm_eff.vcf.gz \
$VCF_PATH/haplotypecaller_filtered_norm_eff.vcf.gz.tbi \
$VCF_PATH/haplotypecaller_filtered_norm_eff_dbsnp.vcf.gz \
$VCF_PATH/haplotypecaller_filtered_norm_eff_dbsnp.vcf.gz.tbi \
$VCF_PATH/freebayes_filtered_norm_eff.vcf.gz \
$VCF_PATH/freebayes_filtered_norm_eff.vcf.gz.tbi \
$VCF_PATH/freebayes_filtered_norm_eff_dbsnp.vcf.gz \
$VCF_PATH/freebayes_filtered_norm_eff_dbsnp.vcf.gz.tbi \
$VCF_PATH/deepvariant_filtered_norm_eff.vcf.gz \
$VCF_PATH/deepvariant_filtered_norm_eff.vcf.gz.tbi \
$VCF_PATH/deepvariant_filtered_norm_eff_dbsnp.vcf.gz \
$VCF_PATH/deepvariant_filtered_norm_eff_dbsnp.vcf.gz.tbi