对于SNP2来说ref 则为 major,alt 为minor。 第三组 关联检验的 reference (non-risk 或者 non-effect)与 risk/effect allele 在这里的概念再次改变,同样的reference allele,在与 risk/effect allele并列时,则指的是GWAS关联检测中的reference allele (non-risk 或者 non-effect),也就是效应量beta(或odds ratio...
alternative (alt) allele是effect allele reference (ref) allele是other allele
( defined $col_idx{tumor_seq_allele1} or defined $col_idx{tumor_seq_allele2} ) or die "ERROR: At least one MAF column for Tumor_Seq_Allele must be defined!\n"; # Fetch all tumor-normal paired IDs from the MAF, doing some whitespace cleanup in the same step my $tn_idx = $col...
Even for HOM_REF genotypes where there are no ALT reads. And thus lead to a GATKCutoffSNP label to be set to the variant. The formula does seem to be applied to the first sample in the VCF, even if the first sample has a HOM_REF genotype. See this example of variants / single ...
Forest plot: Effect of rs16969968*G on CPD. Forest plot of the association between rs16969968 and CPD in each study of the TAG Consortium, each consortium, and meta-analysis across the three consortia. Nature Genetics: doi:10.1038/ng.571 11 Supplementary Figure 2. Regional plot: CPD ...
不太清楚是不是.vcf格式的文件 如果不是可以liftover转换成vcf格式的文件 该有的都会有 ...