VCF Annotation & Filtering - SnpEff & SnpSift(Bcftools)

▶ SnpEff & SnpSift

◆ Install

# Download latest version

>>> wget https://snpeff.blob.core.windows.net/versions/snpEff_latest_core.zip

 

# Unzip file

>>> unzip snpEff_latest_core.zip

 

◆ Usage

※  Reference SNP.vcf가 .gz(압축파일)일때

>>> tabix -p vcf reference_snp.vcf.gz

 

● dbSNP 정보 추가(ID, INFO)

>>> java -Xmx16g -jar snpEff/SnpSift.jar annotate reference_snp.vcf(.gz)

 input.vcf > output.vcf

 

※  Reference Database Check

>>> java -jar snpEff.jar databases | grep "GRCh38"

 

● Annotation(INFO; Variant, Gene, etc..)

>>> java -Xmx16g -jar snpEff/snpEff.jar GRCh38.[Reference Database version] input.vcf > output.vcf

 

● Filtering

>>> java -jar snpEff/SnpSift.jar filter '[조건; ex) ! exists ID. QUAL>=20, FILTER=="PASS"]' input.vcf > output.vcf

 

▶  Bcftools(Filtering)

◆ Install

>>> conda install bioconda::bcftools

 

◆ Usage(Filtering)

>>> bcftools view -i 'FILTER=="PASS"' input.vcf -o output.vcf