VCF学习笔记

关于VCF文件格式的说明：

https://gatk.broadinstitute.org/hc/en-us/articles/360035531692-VCF-Variant-Call-Format

0 for the REF allele, 1 for the first ALT allele, 2 for the second ALT allele, etc. When there is a single ALT allele (by far the more common case), GT will be either:

0/0 : the sample is homozygous reference

0/1 : the sample is heterozygous, carrying 1 copy of each of the REF and ALT alleles

1/1 : the sample is homozygous alternate

| means that the genotypes have been phased杂合的两个等位基因知道哪个等位基因来自哪条染色体；如果是单个样本感觉是可以通过碱基的测序深度获得（Physical Phasing）小局部连成一个整体，接出完整的单倍体，或者是通过测序reads，另外可以如果是trio的化可以通过家族亲缘关系进行推断

https://zhuanlan.zhihu.com/p/36289359

/ means it has not been phased

代表这个位置存在变异也可能不存在变异就是不确定，因此在数据分析的时候一般会去掉