Sentence examples for variants we extracted from inspiring English sources
To derive pronunciation variants, we extracted context-dependent rewrite rules from an alignment of canonical and realized phonemic representations of non-native speech from the JASMIN corpus (the test material was excluded).
To find more reliable variants, we extracted the sequence variants with their bi-directional 50-mer flanking sequences and confirmed that the sequence variants were detected in the flanking regions of the SP3B assembly using the in-house perl script.
To test the performance of each method on a purely non-exonic, non-coding clinical dataset (as the ClinVar data used in the GWAVA paper include synonymous, non-synonymous and UTR exonic variants), we extracted 58 such variants directly from the ClinVar database and generated a background set matched by distance to the nearest TSS, 100 times the size of the true positive set.
To add the functional significance of each variant, we extracted gene structural annotations and SNP functional annotations from a downloaded flat file from UCSC genome.
To enhance the variant information, we extracted variant, phenotype, and literature data from the downloaded flat files of UniProt.
By comparing predictions for variants for which commonly applied methods disagreed, we extracted variants that were difficult to classify.
Following the ACMG recommendations for reporting of incidental next generation sequencing findings, we extracted variants in 56 genes from the exome sequence data of 543 subjects and determined the reportable incidental findings for each participant.
From the variant call format file, we extracted the mean allele frequency across SNPs for each supercontig.
We extracted the variant call results, and tested the variants at the loci covered by Omni 2.5-8.
We extracted rare variants that occurred in less than 5% of the samples and grouped them by population.
(4) Set of mutations with unknown disease relation : We extracted 251,414 variants (28,913 proteins) without known disease associations.
