Next, we map the RNA-seq reads to this HLA-personalized genome, we remove PCR duplicates and we count the number of uniquely mapped reads to each HLA cDNA allele. Extended Data Fig. 6 Allelic fraction replication in HLA gene quantifications. Allelic fraction over time for the 3 HLA class ...
Efficiently inferring the demographic history of many populations with allele count data. bioRxiv. 2018.John A. Kamm, Jonathan Terhorst, Richard Durbin, and Yun S. Song. Efficiently infer- ring the demographic history of many populations with allele count data. bioRxiv, 2018. https://doi.org...
Conversely, 94.7% of singleton (allele count (AC=1) and 55.0% of rare (AC小于1 and MAF...
is the mean allele count of the snp used for the centering, and that \(\sqrt {2p_{j} \left( {1 - p_{j} } \right)}\) is the standard deviation used for the scaling. since \({\mathbf{w}}\) contains scaled allele counts, the estimated snp effects are not ase, i.e., they...
glactools is a set of command-line tools for the management of Genotype Likelihood (GL) and Allele Counts (AC).Descriptionglactools is a suite of utilities to:convert various file formats (VCF,BAM,23andme) into genotype likelihood (GLF) or allele count (ACF) files. GLF files contains ...
final AlleleList<Allele> alleleList = new IndexedAlleleList<>(alleles); if (alleleList.alleleCount() != alleles.length) throw new SkipException("repeated alleles, should be infrequent"); return alleleList; } 代码示例来源:origin: samtools/htsjdk ...
方法名:getMissingAlleleCount VariantStats.getMissingAlleleCount介绍 暂无 代码示例 代码示例来源:origin: opencb/opencga publicDocumentconvertToStorageType(VariantStatsvs){ // Basic fields DocumentmongoStats=newDocument(MAF_FIELD,vs.getMaf()); mongoStats.append(ALT_FREQ_FIELD,vs.getAltAlleleFreq()); ...
publicintcountAllele(finalAlleleallele){ intc=0; for(finalAllelea:getAlleles()) if(a.equals(allele)) c++; returnc; } 代码示例来源:origin: samtools/htsjdk /** * Returns how many times allele appears in this genotype object? * * @param allele ...
scAlleleCount requires python2 with the pandas, pysam, scipy and numpy modules. These are common modules that your administrator has probably already installed. If you don't have them installed the fastest way to get a suitable environment is to install anaconda. ...
In addition, SE33 was observed to have the highest number of distinct allele count for all ethnic populations, regardless of the number of contributors in the DNA mixture profile. The typical number of distinct allele counts observed were six, seven, and eight alleles for a 3-, 4- and 5-...