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See Tables S2 and S3 in Supplement 1. Genotype calling was conducted using the CHIAMO algorithm (64,65) modified for use with the Affymetrix 6.0 genotyping array.
The raw cDNA sequence base calling was conducted by using Phred [12] with a cut-off score of Q20.
Following base calling, alignment and SNP calling was conducted using the ABI Bioscope vs. 1.2.1 (Applied Biosystems), with standard parameter settings for targeted resequencing.
Allele calling was conducted automatically with the Genemapper software and controlled visually.
Briefly, the fragment size calling was conducted using automatic algorithm in FPminer.
Then, variant calling was conducted using the GATK Unified Genotyper [ 11].
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These "waves," as they were called, were conducted in 1975/76, 1983, 1989/90 and 1993 and were funded by the National Institute on Drug Abuse.
Mapping and polymorphic site calling were conducted as described in the resequencing analysis above except that the procedure for filtering duplicated reads using Picard was eliminated because we did not amplify DNA library by PCR.
Sequencing was performed using a 2 × 300 paired-end configuration and image analysis and base calling were conducted with the MiSeq Control Software embedded in the MiSeq instrument.
Image analysis and base calling were conducted with the Illumina pipeline (1.8.2).
Image analysis, signal processing, and base calling were conducted using Newbler 2.3 software (454 Life Sciences Corp ,Branford, CT, USA).
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