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Pipeline publication

[…] exome capture above, except that genomic DNA was sheared to a larger target size and hybrid capture was not performed. Resulting libraries were size selected to contain fragment insert size of 380bp±20% (DGI, FUSION, KORA) and 420bp±25% (UKT2D) using gel electrophoresis or the SAGE Pippin Prep (Sage Science, USA). Libraries were qPCR quantified, pooled, and sequenced with 101bp paired-end reads using Illumina GAII or HiSeq 2000 sequencers to ~5-fold mean coverage., Genotyping was performed by the Broad Genetic Analysis Platform. DNA samples were placed on 96-well plates and genotyped using the Illumina HumanOmni2.5-4v1_B SNV array., Sequence data were processed and aligned to hg19 using the Picard (broadinstitute. github.io/picard/), BWA, and GATK, pipelines. Resulting BAM and VCF files were submitted to NCBI and are available in dbGaP (accession number phs000840.v1.p1, study name NIDDK_GoT2D)., We excluded 151 exome samples with average coverage ≤20x in >20% of the target bases and 68 genome samples with average coverage ≤5x. After sequence alignment and post-processing, aligned sequence reads were screened based on multiple QC criteria, including number of mapped reads, number of mapped bases with <1% estimated base call error rate (>Q20), fraction of duplicate reads, fraction of properly paired reads, distribution of insert sizes, distribution of mean base quality with respect to sequencing cycles, and GC bias ()., We […]

Pipeline specifications

Software tools Picard, BWA, GATK