Sentence examples for use the genome analysis from inspiring English sources

We use the Genome Analysis Tookit's version 1.0.2885 "DepthOfCoverage" to determine average coverage over specified intervals and utilize the histogram output to calculate the percent of bases reaching various coverage thresholds.

SNP and InDel calling was performed using the Genome Analysis Toolkit (GATK, version 2.4-9 52.

SNP calling was subsequently performed using the genome analysis toolkit Unified Genotyper (GATK-UG) algorithm (DePristo et al. 2011).

SNP calling was based on alignment using the Genome Analysis Toolkit 2.0-35 2.0-35 and Picard packaGATK1.71 [ 16].

Determination of heterozygous positions between alleles was performed using the genome analysis toolkit (GATK) Unified Genotyper (31).

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

Base quality score recalibration was performed using the Genome Analysis ToolKit (GATK) [ 18] and QC Failure reads were removed.

Single nucleotide variants (SNVs) were multi-sampled called using the Genome Analysis Toolkit (GATK) v2.7.2 UnifiedGenotyper (DePristo et al., 2011 ).

Quality scores were re-calibrated using the Genome Analysis Toolkit v1.6 [ 24] following the Human 1000 Genome guidelines incorporating information from dbSNP vers.

After recalibration and local realignment using the Genome Analysis Toolkit (GATK version 1.0.5974) [ 15], the refined sequencing results were subjected to variant calling using a toolkit (Atlas2) [ 16].

Local realignment was conducted using the Genome Analysis Toolkit (GATK) [ 37] and SNPs were extracted from the reads alignment file using UnifiedGenotyper, based on multi sample calling.