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Old 10-31-2013, 11:01 AM   #2
Location: California

Join Date: Oct 2013
Posts: 23

The 1000G and 5400ESP projects used different pipelines for sequencing, read mapping and and variant calling, so at least some of the major discrepancies between the listed allele frequencies are due to different quirks in their respective pipelines. For example, each pipeline might consistently map ambiguous reads to a different site in a repetitive or low-complexity region, giving the variant calls in that region a high frequency in one database but not the other.
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