KGGSeq

[…] were 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 Gen […]

[…] on 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 com […]

[…] are. Gene-based association of SNPs with obesity trait level and change will be assessed using VEGAS2 software. Variant annotation and filtering from whole-exome sequences will be performed using the KGGSEQ framework. The association of well-established GWAS SNPs for BMI, WC, WHR and %BF, or a combination of pathogenic mutations in previously identified monogenic genes, with obesity trait level an […]

[…] JA5, we performed exome sequencing in 2 patients, II‐1 and II‐3. In total, 62 960 single‐nucleotide variants and 4192 insertions/deletions (Indels) were detected after stringent quality control using KGGSeq (V0.8), and we chose the top 60 single‐nucleotide variants (listed in Table ) for validation according to their predicted pathogenic probability. It turned out that 2 missense single‐nucleotide […]

[…] 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 for prioritizat […]

[…] within the exome regions included by wANNOVAR and those with allele frequency ≥0.05 in 1000 Genome project or ExAC database []. Pathogenicity prediction of nonsynonymous variants was performed using KGGSeq with default quality control criteria (--gty-qual 20 --gty-dp 4), additional option to predict Mendelian disease-causing and complex disease-causing variants (--mendel-causing-predict best --db […]