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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., 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