Sentence examples for performed realignment from inspiring English sources

GATK [ 18, 19] v2.7-2 performed realignment, base recalibration, variant identification, recalibration and genotyping.

We recalibrated base quality scores and performed realignment around insertions and deletions using the Genome Analysis Toolkit, a framework for analyzing next-generation sequence data [ 27].

Furthermore, we performed realignment to compensate for subject movement, segmentation (Ashburner and Friston 2005), normalization to standard MNI space, and spatial smoothing (8 mm FWHM) using the default settings in SPM8.

Applied Biosytems and Illumina each performed realignments of the D2 and B6 datasets to the public B6 reference sequence [ 7].

Preprocessing was done using FSL software (FMRIB's Software Library, www.fmrib.ox.ac.uk/fsl) and the following steps were performed: (1) Realignment with three-dimensional motion correction.

Slice timing correction was performed after realignment.

To confirm this, we performed BLAT realignment of these ESTs to the zebra finch genome to confirm that they mapped to a single locus.

We removed duplicate reads using Picard MarkDuplicates (v 1.70) [ 46], performed local realignment around indels, base quality score recalibration and variant calling with the Genome Analysis Toolkit (GATK v 2.1.13) 'best practice variant detection method' pipeline [ 1, 47].

For both transcriptome and exome alignments, we further removed duplicates with Picard's MarkDuplicates utility (http://broadinstitute.github.io/picard) (v1.59) and performed local realignment using the GATK's IndelRealigner program [ 22] (v1.4-15 v1.4-15

To correct misalignments arising from indels, we performed local realignments with the Genome Analysis Toolkit Indel Realigner (McKenna et al. 2010).

Genome analysis toolkit 1.4 (GATK) (Nekrutenko and Taylor 2012) was used to perform local realignment of reads to correct misalignments due to the presence of indels ("RealignerTargetCreator" and "IndelRealigner" arguments).