DCM Precision Medicine Study Exomes: Sample SAM1390
Base calls were generated in real-time on the instrument (RTA 2.7.6), and demultiplexed, unaligned BAM files were produced by Picard v1.111 ExtractIlluminaBarcodes and IlluminaBasecallsToSam.   Reads were aligned to the hs37d5(GRCh37) human reference using BWA v0.7.10.  Read-pairs not mapping within ± 2 standard deviations of the average library size (~150 ± 15 bp for exomes) were removed.  Aligned reads were further processed with Picard MarkDuplicates for duplicate removal, GATK v3. 2-2 IndelRealigner for realignment around short insertion-deletions, and GATK v3.2-2BaseRecalibrator for base quality score recalibration.