The Variant Call Format (VCF) specifies the format of a text file used in bioinformatics for storing gene sequence variations.
VCF文件
Variant Call Format(VCF)文件是存储序列变异信息的文本文件，可以表示SNP，插入/缺失，CNV和结构变异。
VCF文件可分为两部分：
- 头文件注释信息
- 变异位点信息
头文件注释信息
以##开头，以key-value键值对的形式记录版本，参考基因组，标签意义等信息
变异位点信息
| 列 | 含义 |
|---|---|
| #CHROM | 参考基因组染色体 |
| POS | 变异位置，1-based |
| ID | 变异ID，如dbSNP中的rs number |
| REF | 参考序列 |
| ALT | 变异序列 |
| QUAL | 变异质量，Phread-scaled，-10 * log prob (ALT is wrong) |
| FILTER | 过滤状态 |
| INFO | 变异的详细信息，其TAG在头注释文件有说明 |
| FORMAT | GT:DP |
INFO
- AA : ancestral allele
- AC : allele count in genotypes, for each ALT allele, in the same order as listed
- AF : allele frequency for each ALT allele in the same order as listed: use this when estimated from primarydata, not called genotypes
- AN : total number of alleles in called genotypes
- BQ : RMS base quality at this position
- CIGAR : cigar string describing how to align an alternate allele to the reference allele
- DB : dbSNP membership
- DP : combined depth across samples, e.g. DP=154
- END : end position of the variant described in this record (for use with symbolic alleles)
- H2 : membership in hapmap2
- H3 : membership in hapmap3
- MQ : RMS mapping quality, e.g. MQ=52
- MQ0 : Number of MAPQ == 0 reads covering this record
- NS : Number of samples with data
- SB : strand bias at this position
- SOMATIC : indicates that the record is a somatic mutation, for cancer genomics
- VALIDATED : validated by follow-up experiment
- 1000G : membership in 1000 Genomes
FORMAT
- GT, genotype, 0 for the reference allele (what is in the REF field), 1 for the first allele listed in ALT, 2 for the second allele list in ALT and so on.
- / : genotype unphased
- | : genotype phased
- DP : read depth at this position for this sample
- FT : Filter flag
- GL : Genotype likelihoods
- GLE: Genotype likelihoods of heterogeneous ploidy
- PL : phred-scaled genotype likelihoods
- GP : phred-scaled genotype posterior probabilities
- HQ : haplotype qualities
- PS : phase set
- PQ : phasing quality
- EC : expected alternate allele counts
- MQ : RMS mapping quality
