Refined variant calling pipeline on RNA-seq data of breast cancer cell lines without matched-normal samples

Here, variants of 29 breast cancer cell lines were called on RNA-seq data via HaplotypeCaller. Low read depth sites, RNA-edit sites, and low complexity regions in coding regions were excluded. Common variants were filtered using 1000 genomes, gnomAD, and dbSNP data. Starting from hundred thousands of single nucleotide variants and small insertions and deletions, about thousand variants remained after filtering for each sample. Extracted variants were validated against the Catalogue of Somatic Mutations in Cancer (COSMIC) for 10 cell lines included in both data sets. Approximately half of the COSMIC variants were successfully called. Importantly, missing variants could mainly be attributed to sites with low read depth. Moreover, filtered variants also included all 10 cancer gene census COSMIC variants, a condensed hallmark variant set.