Fig. 3
Categories of variant calling errors depending on the quality of the alignment. The top panel (a and b) shows the error categories for the high confidence false positives (prediction sets with at least 95% precision). The bottom panel (c and d) shows the error categories for the high-frequency false negatives (ground truth allele frequency ≥25%). The left panel (a and c) displays the error sources when running default bowtie2 alignments, and the right panel (b and d) displays the error sources when running more sensitive alignments, which were performed with parameters —very-sensitive -k 20, and then choosing the primary alignment for each read with several alignments (samtools view -F 256), i.e. the “best” option. The definition of the categories can be found in Section “Analysis of error sources”