Sentence examples for realignment was done from inspiring English sources

Duplications were removed via Picard v1.93, and local realignment was done by GATK v2.4-7.

InDel realignment did not heavily reduce the number of SNVs identified by SAM compared to PL or UG, indicating that SAM effectively removed false positives prior to IR with GATK (only 1,518 less SNVs were identified with SAM when InDel realignment was done prior to variant detection).

Next, realignment is done for motion correction followed by spatial normalization onto the Montreal Neurological Institute (MNI) space (3-mm isotropic voxels).

Base quality recalibration and indel realignment were done with the help of GATK (DePristo et al., 2011).

A small realignment in LaGrange County was done in 2005, in which the roadway was straightened.

Realignment and recalibration was done using the following settings within the software.

Realignment of vectorized serial sections was done as follows.

Realignment to the U.S. National Glycohemoglobin Standardization Program (NGSP) values was done according to a national consensus document for the harmonization of A1C in Spain (9) using the following formula: NGSP = 0.985 × JDS/JSCC + 0.46.

Sequence realignment around insertion/deletions (INDEL) and variant calling was done using the Genome Analysis Toolkit v1.6.

Local realignment around indels and base quality score recalibration was done for each sample, and variants were called by a unified genotyper in GATK-1.3.

Realignment around insertions and deletions, quality score recalibration and variation calling was done using GATK (29, 30).