eSNV-detect

[…] in expression levels; and 4) rna editing sites being confused as dna mutations., currently there are at least variant callers that accept rna-seq data: radia, seurat, vardict, varscan2, snpir, and esnv-detect , , , , , . radia and seurat do not analyze rna-seq data alone, but integrate rna-seq with matched tumor-normal dna from the same patient to improve the accuracy. radia showed that real […]

[…] expression of two alleles, we first need to identify genes with heterozygous snps. there are software programs that can call snps from bulk rna-seq datasets, such as gatk [], samtools [], and esnv-detect []. however, they usually do not work as well on rna-seq data as they do on genomic sequencing data, because the assumption of a 1:1 ratio of the two parental alleles are often violated […]

[…] genotype calling algorithms for snvs were designed for germline dna and not for rna. hence, the false detection rates to call an snv are high in rna-seq data from tumors. we have developed an esnv-detect (expressed single nucleotide variant detection) workflow with parallel alignment strategies (bowtie and bwa). the advantage of using two aligners in esnv-detect is that we take […]