SNVer

[…] and reverse orientation within 500bp of each other) or with mapping quality <10. retained reads were used to detect single nucleotide polymorphisms (snp)., snp calling was carried out using snver []. snps were filtered to remove those called in regions of in the top or bottom 25% of read coverage depth, to remove artefacts caused by misaligned paralogous sequences. variant sites […]

[…] alignments the pipeline reporting the smallest number of snps (294) and vipr on bowtie2 alignments the pipeline reporting the largest number (4354) (a). the average number of indels was 80. vipr and snver were not able to detect any indel and varscan detected indels only from bowtie2 alignments., merging the variants predicted by the different pipelines, a raw dataset of 7925 variants […]

[…] then repaired using a custom script (duke university genome sequencing and analysis core). sequences were aligned to wild-type rat trpv1 using bwa for paired-end reads. variant calls were made using snver., we postulated that sequences from clones categorized as ‘functional’ should not contain any stop codons before the pore domain (q560) and applied a binomial distribution with 95% confidence […]

[…] recalibration, was performed using gatk best practice of broad institute []., at the variant discovery step, the snvs and indels utilized 3 open source callers (unifiedgenotyper [], lofreq [], and snver []) and samsung sds's in-house callers. cnv and translocation were discovered with in-house callers developed by samsung sds. snvs and indels were detected with an ensemble method […]

[…] in gene expression levels., the genes were distributed into categories according to the criteria explained in the results section using homemade python scripts., snp calling was performed using snver software and the mm10 genome as a reference sequence. after calling, all heterozygous snps in the parental m5s and tau-gfp transcriptomes were filtered out. the resulting 27,962 snps were used […]

[…] mutect and vardict, accept single sample as input (). in addition, several algorithms are dedicated to perform single-sample variant calling. these algorithms include snvmix2, shearwater, splinter, snver, outlyzer, pisces, isown, somvarius, and sinvict , , , , , , , , and fall into two categories., snvmix2, shearwater, splinter, snver, outlyzer, and pisces report all variants without […]

[…] tool (v3.00.02; http://www.novocraft.com) with default settings. resulting sam files were converted to bam, and were then sorted and indexed with samtools (v0.1.18; ). mutations were called by snver (v0.5.3; ). since each mixture contains genomic dna of 10 revertants, 10 (or fewer) suppressor mutations, in addition to the original ts mutation, should be identified, with suppressor allele […]

[…] . ), sufficient to identify variants occurring in just one individual, assuming 0.5–1% per base machine error rate., we called 124,541 single nucleotide polymorphisms (snps) using syzygy (84,216) and snver (81,829). for primary analyses, we focused on 41,504 “high-confidence” snps detected by both, with highly correlated allele frequencies (af) (pearson’s ρ = 0.999, p < 2.2 × 10−16; supplementa […]

[…] last accessed may 19, 2017). to call snps and small indels above a threshold frequency of 0.1 and base quality above 20, we employed both frequentist and heuristic methods using respectively snver and varscan (; ). to identify larger indels and other sv, we used pindel and cnvnator (; ). the resulting output files were filtered for duplicates, ancestral variants, and variants found […]

[…] 1000g phase1 and omni 2.5. sequencing coverage is shown in ., variant calling was done only in regions targeted in cancerscan™ v1. we detected snvs using three tools: mutect 1.1.4, lofreq 0.6.1, and snver 0.5.3 [–]. we filtered out falsely detected variants from abnormally aligned strand biased and clustered reads by in-house developed scripts. annovar was used for annotating the detected […]