Sentence examples for for local realignment from inspiring English sources
GATK IndelRealigner was used for local realignment near indels.
(20) Genome Analysis Toolkit(21) was used for local realignment and quality score recalibration.
The Genome Analysis Toolkit [ 46] was used for local realignment around insertion/deletion (indels) regions, and recalibration following the Human 1000 Genome guidelines incorporating information from dbSNP [ 47].
RealignerTargetCreator and IndelRealigner from the GATK version 2.4.7 [ 54] were applied for local realignment around known indels from dbSNP build 133.
Presently, the available software for local realignment is not compatible with the length and the high indel rate of Pacific Biosciences data, but we anticipate the development of new tools.
In brief, the RealignerTargetCreator and the IndelRealigner tools were used for local realignment around indels, the BaseRecalibrator and the PrintReads tools were used for quality score recalibration, the UnifiedGenotyper tool was used for variant calling, and the VariantRecalibrator and ApplyRecalibration tools were used for variant quality score recalibration.
Mapping was improved by two rounds of local realignment.
Use of local realignment and BAQ in the same processing pipeline should be avoided.
Reads were aligned to the human reference sequence hg19 using the Burrows–Wheeler Aligner, and the Genome Analysis Toolkit was used for base recalibration, local realignment and variant calling, following published best practice guidelines, and as described previously [ 22].
The SOLiD BAM files were locally realigned using the GATK local realignment utility [ 2].
Total cost was $528 including storage ($95 for 4104 GB disk space over 7 days), computing ($17 for Elastic Block Storage I/O and $270 for CPU time, 52% for read mapping, 38% for base call quality score recalibration and local realignment, 10% for variant calling) and data transfer (upload is free, and downloading 1.1 TB costs $146).
