BCF2 Quick Reference (r198)

In BCF2, each key in the FILTER, INFO and FORMAT fields is required to be defined in the VCF header. For each record, a key is stored as an integer which is the index of its first appearance in the header. ‘ PASS’ is always indexed at 0, which is special cased as VCF does not require the presence of this word.

In BCF2, a typed value consists of a typing byte and the actual value with type mandated by the typing byte. In the typing byte, the lowest four bits give the atomic type. If the number represented by the higher 4 bits is smaller than 15, it is the size of the following vector; if the number equals 15, the following typed integer is the array size. The highest 4 bits of a Flag type equals 0 and in this case, no assumptions can be made about the lower 4 bits. The table below gives the atomic types and their missing values:

Bit 0–3 C type Missing value Description
1 int8_t 0x80 signed 8-bit integer
2 int16_t 0x8000 signed 16-bit integer
3 int32_t 0x80000000 signed 32-bit integer
5 float 0x7F800001 IEEE 32-bit floating pointer number
7 char ' 0' character

A genotype (GT) is encoded as an integer vector with each integer describing an allele and its phase w.r.t. the previous allele. The first allele does not carry the phase information. In the vector, each integer is organized as ‘ allele+1 1 phased’ where allele is set to -1 if the allele in GT is a dot ’.’ (thus the higher bits are all 0). The vector is padded with missing values if the GT having fewer ploidy.

A BCF2 file is BGZF compressed and all multi-byte value are little endian.

Field Description Type Value
magic BCF2 magic string char[5] BCF 2 1
l_text Length of the header text, including any NULL padding uint32_t
text NULL-terminated plain VCF header text char[l_text]
List of VCF records (until the end of the BGZF section)
l_shared Data length from CHROM to the end of INFO uint32_t
l_indiv Data length of FORMAT and individual genotype fields uint32_t
CHROM Reference sequence ID int32_t
POS 0-based leftmost coordinate int32_t
rlen Length of reference sequence int32_t
QUAL Variant quality; 0x7F800001 for a missing value float
n_allele_info n_allele 16 n_info uint32_t
n_fmt_sample n_fmt 24 n_sample uint32_t
ID Variant identifier typed str
List of alleles in the REF and ALT fields (n=n_allele)
allele A reference or alternate allele typed str
FILTER List of filters; filters are defined in the dictionary typed vec
List of key-value pairs in the INFO field (n=n_info)
info_key Info key, defined in the dictionary typed int
info_value Value typed val
List of FORMATs and sample information (n=n_fmt)
fmt_key Format key, defined in the dictionary typed int
fmt_type Typing byte of each individual value, possibly followed by a typed int for the vector length uint8_t+
fmt_value Array of values. The information of each individual is concatenated in the vector. Every value is of the same fmt_type. Variable-length vectors are padded with missing values; a string is stored as a vector of char. (by fmt_type)