provide tools to view or convert these files, while specialized online VCF editors allow you to upload, modify, and download the updated version. Raw Text Editing:
vcftools --vcf input.vcf --min-alleles 2 --max-alleles 2 --recode --out biallelic vcf edit
bcftools norm -m -any input.vcf > split.vcf provide tools to view or convert these files,
After any , always validate:
# Example: Change "PASS" to "LowQual" in FILTER column for rows with QUAL < 50 bcftools view -h input.vcf > header.txt bcftools view -H input.vcf | awk 'BEGINOFS="\t" if($6<50) $7="LowQual"; print' > body.txt cat header.txt body.txt > edited.vcf split.vcf After any
# Remove indels (edit by variant type) vcftools --vcf input.vcf --remove-indels --recode --recode-INFO-all --out snps_only
This long-form guide explores everything you need to know about VCF editing, from simple manual fixes for individual files to advanced software solutions for batch processing thousands of contacts.