SNVer

[…] nt 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 distinguishing somatic and germline. SNVMix2’s, like JointSNVMix2 and Virmid, infers the posterior probability of each genotype. Shearwater is s […]

[…] y Illumina GAII or Illumina HiSeq2000. Sequencing reads were aligned and processed by Picard analysis pipeline (http://broadinstitute.github.io/picard/). Variants and AFs were called using Syzygy and SNVer. We used ANNOVAR to annotate variants for RefSeq genes (hg19), GERP scores, ENCODE DHS cluster, and 1000 G data. […]

[…] and 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 that integrate […]

[…] picard/; 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 in the […]

[…] ignment, base quality score recalibration, and removal of duplicate reads were performed using GATK and Picard. Single nucleotide variations (SNV) and INDELs were independently detected by MuTect and SNVer. […]

[…] y allelic variations in the two pools, we first mapped the sequence reads to the reference genome and then used four different variant calling tools, SAMtools, Freebayes, GATK’s UnifiedGenotyper, and SNVer. We decided to use more than one variant calling tool, owing to the reported low concordance between different variant calling methods. We utilized variants identified from the six individually […]