New Features
VCFX_validator now includes comprehensive GATK-compatible validation checks:
- ALT allele observation (ALLELES validation) - warns when ALT alleles are not observed in any sample genotype
- Empty VCF detection - header-only files now fail by default (use
--allow-emptyto override) - Header Type/Number validation - validates INFO/FORMAT field definitions
- Variant sorting check - ensures records are sorted by CHROM and POS (disable with
-S) - AN/AC consistency - validates allele count consistency in strict mode (CHR_COUNTS)
- REF validation - check REF alleles against FASTA reference (
-R) - dbSNP ID validation - validate variant IDs against dbSNP (
-D) - GVCF validation - GVCF-specific format checks (
-g) - New
-i/--inputflag - explicit mmap file input option
Performance
- Maintained ~110 MB/s throughput with all new validations enabled
- 1.26x faster than bcftools for validation on benchmark dataset
Full Changelog
See CHANGELOG.md for details.