SnpEff

[…] This included de novo assembly at each potential variant locus. Variants were annotated and analysed using Ingenuity Variant Analysis (IVA) software (QIAGEN, Redwood City, CA, USA), MutationTaster2, SnpEff, SeattleSeq annotation server, and Galaxy (via usegalaxy.org). Allele frequencies and additional annotations were drawn from 1000 Genomes project, NHLBI GO Exome Sequencing Project (ESP), Seatt […]

[…] recalibrator steps on the SNPs and indels. The resulting VCF files were then filtered for high-quality heterozygous SNPs in the non-parental samples. The final list of variants as annotated using the SnpEff tool (version 4.0), setting the source genome to ‘hg19‘.Construction of parental genomes: High quality (PASS filter tag), heterozygous SNPs from each fetus and high quality homozygous SNPs of t […]

[…] chment Kit (Agilent Technologies, California). Sequence reads obtained were mapped to the human genome GRCh37/hg19 assembly using the BWA software and analyzed by the Picard-tools-1.118, GATK.v4, and SnpEff_v4.1.software.[–] The mean depth of target regions was 141X. Variants were annotated using dbSNP142, 1000 Genome, ESP, ClinVar, and our in-house database. Finally, candidate pathogenic variants […]

[…] kat were also found in ClinVar, but the annotations do not contain gene information and are generally less informative (Additional files  and ). Moving from established to predicted effects, we used SnpEff to predict the functional consequences of the GATK-called small variants. SnpEff identified 9997 synonymous and 10,984 nonsynonymous mutations. Among the nonsynonymous mutations, 252 variants a […]

[…] es: -window 35 -cluster 3 -filterName FS -filter “FS > 30.0” -filterName QD -filter “QD < 2.0.” Multisample variant call format (VCF) files were generated using FermiKit (). SNPs were annotated using snpEff (). Polymorphic site positions were analyzed using R package adegenet v.2.0.1 (). […]

[…] al realignment, $REALIGNED is the output from the local realignment and $VFC is the output variant call set in VCF format.To annotate an estimated effect of identified genomic variation, the software SnpEff v4.2 was applied. We used the default parameters and the following command line:java -jar snpEff.jar eff $GFF $VCFwhere $GFF is a previously set up database based on a GFF file and $VCF is the […]