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Method Detail
Submitter Method Handle: EVA_EXAC
Submitter Method ID: EXAC_0.3
Submitted method description:
The current data release (0.3) was initially generated across a combined data set of 91,796 exomes, from which 60,706 were extracted for public release based on consent, consortium permission, exome data quality, and lack of relatedness with other samples
Exome sequencing data was processed through a pipeline based on Picard, using base quality score recalibration and local realignment at known insertion/deletions (indels). We used the BWA aligner for mapping reads to the human genome build 37 (hg19). Geno
GATK Variant Quality Score Recalibration (VQSR) was used to filter variants. To train the SNP VQSR model HapMap3.3 and 1KG Omni2.5 SNP sites were used and a 99.6% sensitivity threshold was used to filter variants, while Mills et. al. 1KG gold standard and

This method was used in the following submission:

Submitter Handle Batch Type Submitter batch id Release build id
EVA_EXAC Frequency EXAC_0.3 144
EVA_EXAC Assay EXAC_0.3 142