For all samples, adapter and low-quality reads were trimmed by Trim Galore (version 0.3.7). Quality checks were performed before and after read trimming by FastQC (version 0.11.4). The trimmed reads were aligned to the human reference genome (GRCh37 with decoy) by BWA mem (version 0.7.10) (44). Duplications were removed using samtools (version 0.1.19) (45). The known indels and single-nucleotide polymorphism (SNPs) were collected from the 1000 Genomes Project (phase 1) and Single Nucleotide Polymorphism Database (dbSNP) (build 144). Then, the reads around known indels were locally realigned, and their base quality scores were recalibrated on the basis of known indels and SNVs, both via the Genome Analysis Toolkit (GATK, version 3.5.0) (46).

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