Improved SNV Discovery in Barcode-Stratified scRNA-seq Alignments.

ABSTRACT: Currently, the detection of single nucleotide variants (SNVs) from 10 x Genomics single-cell RNA sequencing data (scRNA-seq) is typically performed on the pooled sequencing reads across all cells in a sample. Here, we assess the gaining of information regarding SNV assessments from individual cell scRNA-seq data, wherein the alignments are split by cellular barcode prior to the variant call. We also reanalyze publicly available data on the MCF7 cell line during anticancer treatment. We assessed SNV calls by three variant callers-GATK, Strelka2, and Mutect2, in combination with a method for the cell-level tabulation of the sequencing read counts bearing variant alleles-SCReadCounts (single-cell read counts). Our analysis shows that variant calls on individual cell alignments identify at lea

SUBMITTER: N M P 

PROVIDER: S-EPMC8535975 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature