Fig. 2
From: Improving somatic exome sequencing performance by biological replicates
Read and mapping statistics of 12 SEQC2 exomic replicates for 6 centers. X-axis shows the center name, replicate number, and sample type (T: tumor & N: normal) of replicates, separated by underscores. For this calculation, the Qualimap bamqc tool was used in the high-confidence exome region of the marked duplicates BAM files. For the number of reads and mapped reads, we used their global values in Qualimap, while for coverage, we used the mean coverage inside of regions value. Marked duplicates BAM files were generated as an input for Qualimap resulting from the following steps in order in the pipeline: trimming, bwa mapping, sorting, indexing, and marked duplicates