Sentence examples for realigned locally from inspiring English sources

Indels were realigned locally using GATK (www.broadinstitute.org/gatk/) (McKenna et al., 2010), and variants were called from the pileup file using the Varscan software (varscan.sourceforge.net) (Koboldt et al., 2012).

The SOLiD BAM files were locally realigned using the GATK local realignment utility [ 2].

GATK realignment was used to realign reads locally in areas surrounding insertions and deletions (indels) [ 22, 23].

Resulting BAM files were locally realigned using GenomeAnalysisTK-3.1-1 (GATK) Indel-realigner [ 16] tool to minimize the mismatches across the reads.

In 1993 the Greater London boundary, to the east of Cranham and north of the railway line, was locally realigned to the M25 motorway, returning some mostly unpopulated areas of open land to Essex and leaving North Ockendon as the only part of Greater London outside the bounds of the motorway.

The mapped reads were locally realigned using GATK RealignerTargetCreator.

The locally realigned BAM files were used to detect CNV.

Uniquely mapping nonduplicate read pairs were locally realigned with Genome Analysis Toolkit.

Reads were locally realigned around Indels, and raw variants (Single nucleotide variants and Indels) were called using GATK Unified Genotyper [ 36, 37].

The aligned BAM [ 26] files were locally realigned using the Genome Analysis Toolkit (GATK) [ 27] developed by the Broad Institute.

For exome sequencing data, reads were already mapped, locally realigned and recalibrated by the 1,000 Genomes Project.