Variant annotation file format

The variant annotation file contains annotations about the variants. Information such as batch-specific and across-batches INFO scores, allele counts, allele numbers, allele frequencies etc.

The column types are listed here:

Column name	Description
#variant	variant id, formatted as CHROM:POS:REF:ALT
chr	variant chromosome
pos	position
ref	reference allele
alt	alternate allele
AC	allele count
AC_Het	Heterozygote allele count
AC_Het_*	Batch-specific heterozygote allele count
AC_Hom	Homozygote allele count
AC_Hom_*	Batch-specific homozygote allele count
AF	allele frequency
AF_*	Batch-specific allele frequency
AN	Allele number
CHIP_*	Batch-specific Chip genotyped variant marker
HWE_*	Batch-specific Hardy-Weinberg test
INFO	imputation INFO score
INFO_*	Batch-specific imputation INFO score
NS	Number of samples with data
NS_*	Batch-specific number of samples with data
gene_most_severe	gene affected by the most severe consequence
most_severe	most severe consequence as predicted by VEP
rsid	rsid(s) of the variant
b37_coord	Build 37 (hg19) coordinates for variant
EXOME_enrichment_*	variant enrichment in Finnish population against multiple non-Finnish populations (non-Finnish Europeans (nfe), non-Finnish, Non-Swedish Europeans, (nfse), non-Finnish,non-Estonian Europeans (nfee), non-Finnish, non-Swedish, non-Estonian Europeans (nfsee) ) . Allele frequencies taken from gnomAD 2.1 exome data.
EXOME_AF_*	Allele frequencies for different populations, from gnomAD 2.1 exome data.
GENOME_enrichment_*	variant enrichment in Finnish population against multiple non-Finnish populations (non-Finnish Europeans (nfe), non-Finnish,non-Estonian Europeans (nfee)) . Allele frequencies taken from gnomAD 2.1 exome data.
GENOME_AF_*	Allele frequencies for different populations, from gnomAD 2.1 genome data.