Sentence examples for local realignment from inspiring English sources

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

The pipeline consisted of local realignment around INDELs (RealignerTargetCreator and IndelRealigner), quality score recalibration (CountCovariates and TableRecalibrator) and finally variant calling (UnifiedGenotyper).

The reads were realigned using the local realignment tool in Strand NGS.

To further increase the local realignment accuracy, after local realignment, we performed base quality score recalibration on the realigned BAM files using GATK's recalibration tool.

Local realignment around small insertions and deletions (indels) was performed, using GATK's indel realigner to minimize the number of mismatching bases across all reads.

GATK IndelRealigner was used for local realignment near indels.

Local realignment and reassembly, and use of spanning reads, resolved a further 40 gaps.

Local realignment and base quality score recalibration were done using GATK.

Then, local realignment was done with an in-house short reads aligner with a small seed size (k = 11) (Qgram-SmithWaterman).

ADAM provides tools to sort reads, remove duplicates, do local realignment, and do base quality score recalibration.

This was followed by local realignment with GATK [ 12].