KGGSeq

[…] analysable alterations (some variants mapped to more than one transcript) and three variants were predicted to be disease-causing. only one variant was predicted to be mendelian disease-causing by kggseq ()., among the shortlisted variants, only the hspb1 non-synonymous snp variant has a homozygous genotype and is compatible with the autosomal recessive inheritance demonstrated in the pedigree […]

[…] analysis with mutationtaster identified 199 analysable alterations, and three variants were predicted to be disease-causing. again, only one variant was predicted to be mendelian disease-causing by kggseq ()., the heterozygous gdap1:nm_018972:c.358c>t (p.r120w) variant was initially reported as a mutation in autosomal recessive form of cmt [], and was later found also in the autosomal […]

[…] are implemented in c++), this algorithm substantially improved the speed of loading and parsing text data. we believe this algorithm will also be useful for other bioinformatics analysis tools., kggseq was designed to integrate multiple methods and resources for wgs downstream analysis. although it has integrated abundant functions for a comprehensive downstream analysis into five main […]

[…] and clinvar database (http://www.ncbi.nlm.nih.gov/clinvar/) as well as capitalbio gedd database (capitalbio, beijing, china). the potentially pathogenic variants were evaluated with kggseq (version v0.5) using a logit model to combine prediction scores from multiple methods and to compute an unbiased estimate of the probability of a rare nonsynonymous snv being pathogenic. […]

[…] format file, and variant filtration was performed for both snps and indels to remove low quality and potentially false-positive variants. variant data were annotated using annovar (v 2013aug23) and kggseq (v 0.6)., sanger sequencing of nlrp5 was used to confirm exome variants, establish their inheritance, fill gaps in exome coverage and screen a further 14 patients (four bws–mlid, five […]

[…] processed using the gatk framework [version 2.8.1 ()], according to the gatk best practices recommendations (, ). variants were classified as known or novel based on dbsnp146 and annotated using kggseq ()., annotations included positions in ucsc, refgene, gencode and ensembl transcripts, omim and clinvar annotations, potential false positive signals, allele frequency in dbsnp, esp6500, 1000 […]

[…] variants and estimated per-individual heterozygosity (~inbreeding), pairwise relatedness, and sex-check using plink (additional file : table s1). variants quality control was conducted by software kggseq (http://statgenpro.psychiatry.hku.hk/limx/kggseq/ doc/usermanual.html), which were carefully designed to filter and prioritize gene variants in exome sequencing of rare mendelian and common […]

[…] and the following settings: the indep-pairwise option with a window size of 50, a step of 5 and an r2 threshold of 0.5 [,]., alterations passing quality measurements were annotated with the kggseq and annovar programs [,]. variants were normalized prior to annotation []. ensembl, refseq, and gencode transcripts were all annotated, and the top consequence per gene was used […]

[…] analysis with mutationtaster identified 199 analysable alterations, and three variants were predicted to be disease-causing. again, only one variant was predicted to be mendelian disease-causing by kggseq ()., the heterozygous gdap1:nm_018972:c.358c>t (p.r120w) variant was initially reported as a mutation in autosomal recessive form of cmt [], and was later found also in the autosomal […]

[…] variants with minor allele frequency >0.01 in any of these public databases (dbsnp137, 1000 human genome project, and nhlbi exome sequencing project). an automatic pipeline integrating gatk [], kggseq [], annovar [], and plink [] was used to generate the final set of qualified variants (additional file : figure s1)., rare, exonic variants present in the probands but absent in both parents […]