Strelka

[…] ibration were performed using the Genome Analysis Toolkit (GATK). Somatic single nucleotide variants (SNVs) were identified using MuTect; small insertions and deletions (indels) were identified using Strelka and VarScan 2,, and further curated by manual inspection. Variants found with >5% global minor allele frequency in dbSNP (Build 137) or that were covered by <10 reads in the tumor or <5 reads […]

[…] eads around mutated sites with Novoalign to hg19 including decoy sequences and re-ran MuTect to filter out mutations in problematic regions. To call somatic insertions and deletions (indels), we used Strelka and annotated the mutation consequences using Oncotator. We also filtered out SSNVs and indels present in a panel of normal samples in order to filter out potential germline sites or recurrent […]

[…] transcriptome sequencing (WTS, a.k.a. RNA-seq) data. We calculate the somatic single nucleotide variants (SNVs), insertions and deletions (INDELs), and copy number variations (CNVs) using Mutect [], Strelka [], and EXCAVATOR [], respectively. The MapSplice-RSEM [, ] pipeline was used for RNA-seq quantification to warrant accuracy in spite of long computation time. Galaxy [] pipelines for WES and […]

[…] d candidates that were identical to candidates identified in the control samples, assuming that such sites were the result of sequencing errors and should be classified as false positives (MuTect and Strelka tolerate one or two base-calls of candidate mutations in control samples at default parameters, regarding those as sequence artifacts). Strelka computes an original score called Quality Score […]

[…] nment around indels, and recalibrate base quality scores. The resulting BAM files (one per sample) served as inputs to somatic mutation callers (Fig. ).Two somatic mutation callers (muTect v1.1.7 and Strelka v1.0.14) were used, with default parameters for WES data. Somatic variants called by either method were annotated with functional impact and population frequency using ANNOVAR. We filtered som […]

[…] ing SNV, it calls SNV genotypes independently and its likelihood function assumes no Allelic specific expression (ASE). When read counts are very low, SAMtools/BcfTools may not call SNV genotypes []. Strelka takes as input the sequencing data files of tumor and normal samples in BAM format and by applying a Bayesian probability model define the most likely genotype. Variant detection is also based […]