title: LumA_Y: Sample Sample_PRE_DNA_053
design: Illumina libraries were constructed from sheared tumor and normal genomic DNA (range of 100-250 ng input) using the KAPA Bio library construction kit and Illumina adapter sequences that included 8 bp index sequences on each adapter. A Solid Phase Reversible Immobilization (SPRI) bead cleanup procedure was used to select size fractions between 300-500bp for each library. The resulting libraries were minimally amplified by PCR, pooled in equimolar quantities at 8-9 samples per pool, and captured with the Nimblegen SeqCap EZ Human Exome v3 exome capture reagent. The SPRI purified capture products were amplified by PCR, and quantitated by qPCR.  Each library pool was then diluted and sequenced on an Illumina HiSeq2000 by paired end, 100 bp reads, with an aim to generate 7Gb of paired end read data per sample. Alignments of reads to the human genome reference sequence GrCH37) were evaluated for quality and coverage, requiring at least 70% coverage at 20-fold depth according to the BED file definition of the Nimblegen reagent.  We also evaluated genotype concordance between tumor and normal and required a 90% or higher concordance to evaluate the quality of sequence data coverage.
attributes.tag: alignment_software
attributes.value: bwa (V0.5.9)