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The NIEHS team’s pipeline was applied to WES1, WES2, and WES3 datasets. Raw data from the FASTQ files was preprocessed with cutadapt [62] (v. 1.12) by removing the sequencing adapter and low quality read (Q20), then was aligned to human reference genome (hg19) with BWA-MEM [29] (v0.7.15-r1140) with default parameters (bwa mem -M -t 4 -a -V -T 60 -p). The alignment was post-processed with Picard [56] (v2.9.1) by removing the duplication, then bam files for each tissue were merged (by exome capture vendor platform library). All three batches of whole exome sequencing alignments have gone through an in-houseEnsemble-Variant-Calling pipeline, which contains Samtools [24] (v1.3.1.), Mutect1 [22] (v1.1.4), and VarScan2 [61] (v2.4.3), and the calling was done with default recommended parameters. Whenever the reference genome was needed for variant calling, hg19 was used for WES1, WES2, and WES3. Human SNPs obtained from dbSNP v.146 were used in the variant calling to mask germline variants. Somatic variants were reported according to each exome capture platform vender’s recommended filtering criteria and in conjunction with a minimum read depth of 20.

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