vcf-standardizing-tools

INSTALL

Install picard

git clone https://github.com/broadinstitute/picard.git  
cd picard   
docker build -t picard .  

Install bcftools

wget https://github.com/samtools/bcftools/releases/download/1.9/bcftools-1.9.tar.bz2  
tar yxvf bcftools-1.9.tar.bz2  
make  
make install  

Install htslib

# Visit the following URL
http://www.htslib.org/download/  
# Download
tar yxvf htslib-1.9.tar.bz2  
make  
make install  

Get chain file (Please refer to the credits)

wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz  
guzip hg19ToHg38.over.chain.gz  

Get Reference genome

# Visit the following URL
https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files  
# Download 
GRCh38.d1.vd1.fa.tar.gz  

Create Reference dictionary

docker run \
-v /Users/chibaken/top-gear-vcf-check/ref:/local/ref \
picard CreateSequenceDictionary \
R=/local/ref/GRCh38.d1.vd1.fa \
O=/local/ref/GRCh38.d1.vd1.dict

Run

VCF standardization

cd /Users/chibaken/top-gear-vcf-check/tools/liftover_test/script  
python standard_vcf_mutation.py mutation.vcf mutation_standard.vcf  

liftover

docker run \
-v /Users/chibaken/top-gear-vcf-check/ref:/local/ref \
-v /Users/chibaken/top-gear-vcf-check/output:/local/output \
picard -j "-Xmx8000m" LiftoverVcf \
I=mutation_standard.vcf \
O=mutation_liftover.vcf \
CHAIN=/local/ref/hg19ToHg38.over.chain \
REJECT=mutation_reject.vcf \
R=/local/ref/GRCh38.d1.vd1.fa

VCF sort

bcftools sort mutation_liftover.vcf > mutation_sorted.vcf

Normalize indels

bcftools norm \
--fasta-ref GRCh38.d1.vd1.fa \
mutation_sorted.vcf > mutation_normalize.vcf

VCF check

bash run_vcf-validator.sh vcf-validator \
mutation_normalize.vcf \
output_dir/check_result

bgzip and create index

bgzip mutation_normalize.vcf
tabix -p vcf mutation_normalize.vcf.gz

Reference document

picard (liftover)

https://broadinstitute.github.io/picard/command-line-overview.html#LiftoverVcf

bcftools (norm)

https://samtools.github.io/bcftools/bcftools.html#norm