Sentence examples for base quality scores of from inspiring English sources

VarScan distinguishes errors from true SNVs by examining the individual base quality scores of reads covering the potential SNV.

We used a SNP discovery window of 7 bp at a central base quality score of 40 with surrounding base quality scores of 20 or more.

Indel Realign was executed using the full Smith Waterman alignment algorithm and base quality scores of reads were recalibrated in the aligned.BAM files.

Aligned reads were then realigned around indels and areas of high entropy using GATK (v. 1.0) IndelRealigner, and the base quality scores of realigned reads were then recalibrated using GATK TableRecalibration [ 10].

Next, using the dbSNP database of known variants (Sherry et al., 2001), the BaseRecalibrator module is used to generate co-variation data tables that are then used by the PrintReads module to recalibrate the base quality scores of the aligned reads.

We determined INDELs and realigned reads falling around them using GATK (DePristo et al. 2011), and finally, we recalibrated base quality scores of the aligned reads by considering empirical Phred scores at the level of cycle effect (position in read) and dinucleotide mismatch distribution (the effect of the preceding nucleotide).

The average base quality score for a majority of the data sets in the present study fell within the high confidence range (base quality score of 30 40, green region).

For scoring DNA methylation in our analyses, each individual CpG was required to pass a minimum Phred base quality score of 20 and be covered by at least 8 reads.

The central base quality score of ≥25 and average surrounding base quality score of ≥20 were set to assess the quality of reads at positions for SNP detection.

A minimum mapping quality score of 30 (Phred scale) and base quality score of 15 were set as lower thresholds for variant calling.

In the SNP detection data set, we required a per base quality score of at least 10 if the read was singly represented.