VCF格式详解：基因变异呼叫格式V4.2

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"VCF格式详解.pdf" VCF（Variant Call Format）是一种广泛使用的文本文件格式，用于存储基因组变异数据。VCF版本4.2是该格式的一个历史版本，虽然已被更新至VCFv4.3，但理解VCF的基础结构和内容仍然至关重要。在VCF文件中，信息主要分为三个部分：元信息、头信息和数据行。元信息行以两个连续的井号（##）开头，包含关于文件格式、日期、软件源、参考序列等的描述性信息。例如，文件格式行（##fileformat=VCFv4.2）表明这是VCF格式的4.2版，而文件日期行（##fileDate=20090805）则指定了文件创建的时间。头信息行以一个井号（#）开始，紧接着是列标题，定义了每列的数据含义。VCF的标准列包括CHROM（染色体）、POS（变异位置）、ID（变异标识符）、REF（参考碱基）、ALT（替代碱基）、QUAL（质量分数）、FILTER（过滤状态）、INFO（附加信息字段）和FORMAT（样本格式）。INFO字段包含了如NS（具有数据的样本数）、DP（总深度）和AF（每个ALT等位基因的频率）等统计信息。数据行则对应基因组中的每一个变异位点，每行数据包含了多个样本的基因型信息。例如，REF列表示该位置的参考碱基，ALT列可能包含一个或多个替代碱基。FORMAT列定义了样本列中数据的排列方式，常见的有GT（基因型，表示样本的等位基因状态），AD（等位基因深度，表示每个等位基因的读数）等。 VCF格式允许扩展和自定义，因此可以容纳各种复杂的数据类型，如结构变异、拷贝数变异以及复杂的多等位基因变异。这种灵活性使得VCF成为生物信息学领域分析基因组变异数据的标准格式。然而，由于其复杂性和可扩展性，解析和处理VCF文件需要专门的工具和库，如bcftools、GATK等。在实际应用中，VCF文件通常会经过压缩（如bgzip）并索引（如tabix），以便快速查询和提取特定区域的数据。这使得大型基因组项目能够有效地存储和分享大量的变异数据。 VCF格式是生物信息学中一个至关重要的工具，它提供了一种标准化的方式来描述和交换基因组变异信息，促进了遗传疾病研究、群体遗传学以及精准医学的发展。理解和掌握VCF格式对于处理基因组数据的科学家和工程师来说是必要的技能。

in the GT ﬁeld (for example ‘./.’ for a diploid genotype and ‘.’ for haploid genotype). The meanings of the

separators are as follows (see the PS ﬁeld below for more details on incorporating phasing information into the

genotypes):

◦ / : genotype unphased

◦ | : genotype phased

• DP : read depth at this position for this sample (Integer)

• FT : sample genotype ﬁlter indicating if this genotype was “called” (similar in concept to the FILTER ﬁeld).

Again, use PASS to indicate that all ﬁlters have been passed, a semicolon-separated list of codes for ﬁlters

that fail, or ‘.’ to indicate that ﬁlters have not been applied. These values should be described in the meta-

information in the same way as FILTERs (String, no whitespace or semicolons permitted)

• GL : genotype likelihoods comprised of comma separated ﬂoating point log

-scaled likelihoods for all possible

genotypes given the set of alleles deﬁned in the REF and ALT ﬁelds. In presence of the GT ﬁeld the same

ploidy is expected and the canonical order is used; without GT ﬁeld, diploidy is assumed. If A is the allele in

REF and B,C,... are the alleles as ordered in ALT, the ordering of genotypes for the likelihoods is given by:

F(j/k) = (k*(k+1)/2)+j. In other words, for biallelic sites the ordering is: AA,AB,BB; for triallelic sites the

ordering is: AA,AB,BB,AC,BC,CC, etc. For example: GT:GL 0/1:-323.03,-99.29,-802.53 (Floats)

• GLE : genotype likelihoods of heterogeneous ploidy, used in presence of uncertain copy number. For example:

GLE=0:-75.22,1:-223.42,0/0:-323.03,1/0:-99.29,1/1:-802.53 (String)

• PL : the phred-scaled genotype likelihoods rounded to the closest integer (and otherwise deﬁned precisely as

the GL ﬁeld) (Integers)

• GP : the phred-scaled genotype posterior probabilities (and otherwise deﬁned precisely as the GL ﬁeld); intended

to store imputed genotype probabilities (Floats)

• GQ : conditional genotype quality, encoded as a phred quality −10log

p(genotype call is wrong, conditioned

on the site’s being variant) (Integer)

• HQ : haplotype qualities, two comma separated phred qualities (Integers)

• PS : phase set. A phase set is deﬁned as a set of phased genotypes to which this genotype belongs. Phased

genotypes for an individual that are on the same chromosome and have the same PS value are in the same

phased set. A phase set speciﬁes multi-marker haplotypes for the phased genotypes in the set. All phased

genotypes that do not contain a PS subﬁeld are assumed to belong to the same phased set. If the genotype in

the GT ﬁeld is unphased, the corresponding PS ﬁeld is ignored. The recommended convention is to use the

position of the ﬁrst variant in the set as the PS identiﬁer (although this is not required). (Non-negative 32-bit

Integer)

• PQ : phasing quality, the phred-scaled probability that alleles are ordered incorrectly in a heterozygote (against

all other members in the phase set). We note that we have not yet included the speciﬁc measure for precisely

deﬁning “phasing quality”; our intention for now is simply to reserve the PQ tag for future use as a measure

of phasing quality. (Integer)

• EC : comma separated list of expected alternate allele counts for each alternate allele in the same order as

listed in the ALT ﬁeld (typically used in association analyses) (Integers)

• MQ : RMS mapping quality, similar to the version in the INFO ﬁeld. (Integer)

If any of the ﬁelds is missing, it is replaced with the missing value. For example if the FORMAT is GT:GQ:DP:HQ

then 0 | 0 : . : 23 : 23, 34 indicates that GQ is missing. Trailing ﬁelds can be dropped (with the exception of the GT

ﬁeld, which should always be present if speciﬁed in the FORMAT ﬁeld).

See below for additional genotype ﬁelds used to encode structural variants. Additional Genotype ﬁelds can be

deﬁned in the meta-information. However, software support for such ﬁelds is not guaranteed.

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VCF格式详解：基因变异呼叫格式V4.2

vcf-vcf.tar.gz

vcf-0.9.8.tar.gz

gatk GenotypeGVCFs -R ref.fa -V chrx.merged.g.vcf.gz -O chrx.genotype.vcf.gz各个参数的意义，并举例

怎么用plink软件进行vcf格式转为ped格式

bcftools将vcf生成bgzip和index格式

如何在Linux系统下使用vcftools工具将两个不同样本的vcf文件合并为一个

根据SNP的多态性

报错shapeit --input-vcf hwe.snp.vcf.gz --input-ref /data2/qixb/zhangzh/database/Ref_NGS_need_file/Homo_sapiens_assembly38.fasta --output-phasing hwe_pashing --output-log hwe_pashing.log Phaser mode : unrecognised option '--output-phasing'

#2 gvcf文件按染色体合并 ls chrx.g.vcf.gz > chrx_gvcf.list gatk CombineGVCFs -R ref.fa -V chrx_gvcf.list -L X(染色体号) -O chrx.merged.g.vcf.gz 其中染色体号取什么值，请举例

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