SNVer

[…] 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 […]

[…] 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 […]

[…] . ), 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 […]

[…] 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 […]

[…] 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 […]