Small variants in human breast cancer cell lines
Here, variants of 29 breast cancer cell lines were called on RNA-seq data via HaplotypeCaller. Low read depth sites (<5), RNA edit sites, and low complexity regions (LCRs) were excluded. Common variants were filtered using 1000 genomes, gnomAD, and dbSNP data. Starting from hundred thousands of single nucleotide variants (SNVs) and small insertions and deletions (InDels), a thousand variants remained after filtering for each sample.