BCFv1_qref.tex

Field	Description	Type	Value
magic	Magic string	`char[4]`	`BCF 4`
l_seqnm	Length of concatenated sequence names	`int32_t`
seqnm	Concatenated names, `NULL` padded	`char[l_seqnm]`
l_smpl	Length of concatenated sample names	`int32_t`
smpl	Concatenated sample names	`char[l_smpl]`
l_meta	Length of the meta text (double-hash lines)	`int32_t`
meta	Meta text, `NULL` terminated	`char[l_meta]`

seq_id	Reference sequence ID	`int32_t`
pos	Position	`int32_t`
qual	Variant quality	`float`
l_str	Length of str	`int32_t`
str	`ID+REF+ALT+FILTER+INFO+FORMAT`, `NULL` padded	`char[l_str]`
Blocks of data; #blocks and formats defined by `FORMAT` (table below)

Field	Type	Description
`DP`	`uint16_t[n]`	Read depth
`GL`	`float[n*G]`	Log10 likelihood of data; $G=\frac{A(A+1)}{2}$ , $A=\#\{\textit{alleles}\}$
`GT`	`uint8_t[n]`	`missing 7 \| phased 6 \| allele1 3 \| allele2`
`_GT`	`uint8_t+uint8_t[n*P]`	Generic GT; the first int equals the max ploidy $P$ . If the highest bit is set, the allele is not present (e.g. due to different ploidy between samples).
`GQ`	`uint8_t[n]`	Genotype quality
`HQ`	`uint8_t[n*2]`	Haplotype quality
`_HQ`	`uint8_t+uint8_t[n*P]`	Generic HQ
`IBD`	`uint32_t[n*2]`	IBD
`_IBD`	`uint8_t+uint32_t[n*P]`	Generic IBD
`PL`	`uint8_t[n*G]`	Phred-scaled likelihood of data
`PS`	`uint32_t[n]`	Phase set
Integer	`int32_t[n*X]`	Fix-sized custom Integer; $X$ defined in the header
Numeric	`double[n*X]`	Fix-sized custom Numeric
String	`uint32_t+char*`	`NULL` padded concat. strings (int equals to the length)

A BCF file is in the BGZF format.
All multi-byte numbers are little-endian.
In a string, a missing value ’.’ is an empty C string “ 0” (not “. 0”)
For GL and PL, likelihoods of genotypes appear in the order of alleles in REF and then ALT. For example, if REF=C, ALT=T,A, likelihoods appear in the order of CC,CT,TT,CA,TA,AA (NB: the ordering is different from the one in the original BCF proposal).
Predefined FORMAT fields can be missing from VCF headers, but custom FORMAT fields are required to be explicitly defined in the headers.
A FORMAT field with its name starting with ‘_’ is specific to BCF only. It gives an alternative binary representation of the corresponding VCF field, in case the default representation is unable to keep the genotype information, for example, when the ploidy is not 2 or there are more than 8 alleles.