vcf2avinput

vcf2avinput is a Python script for converting VCF files to ANNOVAR avinput format. It aims to replace convert2annovar in ANNOVAR software. The VCF files generated by following callers are supported：GATK4（mutect2, haplotypecaller), DeepVariant, Strelka, Varscan.

Installation and Dependency

Currently it's only a simple python script so no need to install. Just copy to you folder and run it. Nonetheless it needs vcfpy package to run.

pip install vcfpy

Input and output

It takes a left-normalized and siplited VCF file as input and it outputs an avinput format file. After that you can use ANNOVAR to annotate the avinput file.

table_annovar.pl YOUR_INPUT.avinput [DATA_BASE_FOLDER] -buildver [hg19|hg38] --outfile [OUTPUT_PREFIX] -remove -protocol [DATA_BASE_NAMES] -operation [OPERATION] -nastring . --otherinfo --polish

To make a left-normalized and splitted VCF file you can use bcftools as recommended here

bcftools norm --force -m-both -o ex1.step1.vcf ex1.vcf.gz  # split
bcftools norm --force -f human_g1k_v37.fasta -o ex1.step2.vcf ex1.step1.vcf  # left normalize

Usage

# generate my_sample.avinput
vcf2avinput.py my_sample.vcf

# only extract sample S1
vcf2avinput.py -s S1 my_sample.vcf

# manually assign type as mutect2
vcf2avinput.py -t mutect my_sample.vcf

# show help
vcf2avinput.py -h

Contributing

Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.

Please make sure to update tests as appropriate.

License

MIT