SnpEff

[…] regions in the genome, we visualized these densities with circos (v0.69) []. we used snpsift (v4.2) [], a vcf-manipulation tool, to extract all the genes contained between the snp-densest regions., snpeff was used to annotate variants of the local strains (v4.2, build 2015–12-05) [], classifying them as synonymous or non-synonymous and obtaining their respective impact according […]

[…] to the reference genome of a. laidlawii pg-8a (genbank accession number cp000896) and annotation of single nucleotide polymorphisms (snps) were performed using bowtie2 software (), samtools (), and snpeff version 3.3 (). gene prediction and annotation were performed using the ncbi prokaryotic genome annotation pipeline ()., mutations in the genes associated with the development of tetracycline […]

[…] the mutation allele]/[number of all reads mapped to the loci]) cutoff was set to 1. snps with large effects on genes (missense, nonsense, splice_site_acceptor, splice_site_donor) predicted by snpeff (cingolani et al., ) were retained as candidate causal mutations. the candidate mutations from two allelic f2 populations were then compared to determine the overlap., to analyze […]

[…] local realignment and base quality recalibration were done by the genome analysis toolkit (gatk ver 3.5). variant calling was performed by gatk haplotypecaller. variants were annotated by snpeff ver 4.2. as a result, 1 heterozygous nonsense mutation, c.1956g>a; p.trp652∗ (reference sequence: nm_001024858.2), was identified in the exon 13 of sptb gene (fig. ). this novel mutation […]

[…] using bowtie 2 , (2) the duplicates were marked and sorted using picard, (3) variants were called using samtools and bcftools after indel realignment using gatk, (4) transcripts were annotated using snpeff , (5) functional variants were prioritized for rare variants by comparison against the public databases [dbsnp, nhlbi exome sequencing project exome variant server, and exome aggregation […]

[…] 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), […]

[…] 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 […]

[…] genome assemblies and variant calling were the same except that the variant calling for alignment to v1.2 assembly was not limited to marker positions. the detected snps were then annotated with snpeff [] and the p. patens v1.6 genome annotation []. the gbrowser on phytozome.org provided the cross reference of v3 and v1.6 genome annotations, and the v1.6 annotation of all genes located […]

[…] found in clinvar, but the annotations do not contain gene information and are generally less informative (additional files  and ). table 2 , 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 […]

[…] 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 ()., we used filtered variants (vcf) to visualize relationships between isolates using principal-component […]