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Preprocess of whole-genome sequencing data

XZ Xionghui Zhou
HZ Haizi Zheng
HF Hailu Fu
KM Kelsey L. Dillehay McKillip
SP Susan M. Pinney
YL Yaping Liu
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The adapter was trimmed by Trimmomatic (v0.36) [18] in paired-end mode with the following parameters: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:true MINLEN:36. After adapter trimming, reads were aligned to the human genome (GRCh37, human_g1k_v37.fa) using BWA-MEM 0.7.15 [19] with default parameters. PCR-duplicate fragments were removed by samblaster (v0.1.24) [20]. Only high-quality autosomal reads were used for all downstream analyses (both ends uniquely mapped, either end with a mapping quality score of 30 or greater, properly paired, not supplementary alignment, and not a PCR duplicate). In addition, fragments shorter than 50bp and longer than 1000bp are excluded from downstream analysis.

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