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The aligned reads were realigned at indel positions with the GATK [ 40] IndelRealigner algorithm to enhance the mapping quality.
In order to ensure consistent representation of INDELs, both SOLiD and Illumina BAM files were realigned at runtime using the left alignment utility in the FreeBayes variant caller package (bamleftalign), and were split in cases where mismatches could be resolved by a larger insertion or deletion using gap-opening realignment (ogap) [ 11].
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It was realigned at some point between 1927 and 1932 to follow East Avenue to Rochester instead.
The original bypass plan had PA 402 being realigned at the junction with Oak Grove Drive, onto a new alignment that would have crossed over the Marshalls Creek and terminated at an interchange with US 209 at the northern end of the bypass.
By 1966, PA 73 was realigned at Oley to follow its current alignment west to PA 61 in Leesport, replacing a portion of PA 383 between east of Leesport and Maiden Creek.
At first, all scans were realigned to one mean image, which had been obtained across all conditions, to correct for movement artifacts.
The F-FDG images were realigned to the first F-FDG image and the C-PIB images at baseline and follow-up were co-realigned using the respective F-FDG images as templates.
EPI time series were realigned and spatially smoothed with a cubic Gaussian Kernel of 8mm full width at half maximum.
Aligned reads were realigned to the genome.
Predicted indels were realigned using a Smith Waterman approach21.
The EPI images were realigned spatially [27].
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