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)估计时的参考,概念上与上述ref与alt的组合无关,但为了保持统一性,近年来研究中关联检验的reference 也会与 reference genome保持一致,以避免混淆等。
alternative (alt) allele是effect allele reference (ref) allele是other allele
因此当转化vcf格式时,REF和ALT是按照等位基因频率来进行分配的,部分位点的REF和ALT可能发生调换,即便是使用--keep-allele-order参数也是无用的。 这也是为什么我建议大家简化vcf信息时,不要使用plink和vcf来回转化的方式,而是直接使用bcftools,详见往期推文:如何快速简化vcf信息? 当两个vcf文件合并,位置(CHR+POS)相同...
##3K位点由于是plink1.9转化而来,ref和alt可能发生了调换,需要纠正过来方能合并。比如下面的错误是由于3k.overlap.vcf.gz中的1:715297位点REF和ALT对应的G和A 反了。 $ bcftoolsmergearray.vcf.gz3k.overlap.vcf.gz-Oz-o merge.vcf.gz TheREFprefixes differ: G vs A (1,1) Failedtomergeallelesat1:715297...
因此当转化vcf格式时,REF和ALT是按照等位基因频率来进行分配的,部分位点的REF和ALT可能发生调换,即便是使用--keep-allele-order参数也是无用的。 这也是为什么我建议大家简化vcf信息时,不要使用plink和vcf来回转化的方式,而是直接使用bcftools,详见往期推文:如何快速简化vcf信息?
原因是待处理的vcf,他们的ref allele不一致,所以 解决方法是 bcftools norm 先统一 ref allele 如bcftools norm -c s -f /ldfssz1/ST_BIGDATA/USER/st_bigdata/Sentieon/reference_bigdatacompute/hg38_noalt_withrandom/hg38.fa -o /jdfssz1/ST_HEALTH/P21Z10200N0047/lizhichao/zbolt_test/data_input...
Divide the alternative allele depth of the first sample, by the total sequencing depth of the first sample, and see if that is below 0.25. But is the first sample really representative for all samples? Or what if the first sample is not HET_VAR but HOM_REF or HOM_VAR? Or am I mis...
Albums: Point of Origin, Next to Parallel, Allele Sean Mackin Pop punk, Alternative rock, Punk rock As violinist and backing vocalist for the Jacksonville-based pop-punk band Yellowcard, Sean Mackin's unique fusion of punk rock energy and classical violin melodies have become a defining charact...
MAF=minor allele frequency, HWE=Hardy Weinberg Equilibrium, f=female, m=male. ProbABEL Nature Genetics: doi:10.1038/ng.571 4 Supplementary Table 3. Sample quality control for studies in the TAG Consortium. Study Call rate Population-based cohort studies ARIC >90% BLSA >97% CHS InCHIANTI ...
Results: The distribution of the 4G/5G genotypes was no different in childhood stroke patients and controls, with a 4G allele frequency of 55.8% in patients compared with 53.8% in control subjects (P=0.49). The 4G/4G genotype compared with the remaining genotypes was present in 43 cases and...