Sentence examples for minimum base quality from inspiring English sources

In brief, adapters were removed, paired-end data merged, and reads quality filtered using Clip&Merge78 with a minimum base quality of 20 and a minimum fragment length of 30.

The multisample SNP calling was performed using GenomeAnalysisTK UnifiedGenotyper53: PCR error rate was set to 0.005 (–pcr_error_rate 5.0E 3); we excluded all reads with mate unmapped or mapped to a different marker (–read_filter UnmappedRead, –read_filter BadMate); the minimum base quality considered for variant calling was set to 20 (–mbq 20).

For Capture Validation (CapVal), we used the following algorithm to determine the validation status: First we obtained the mutant and reference allele counts for each marker in the corresponding sample, requiring a minimum base quality of 15 for SNVs and 5 for indels.

For SNPs other than the high confidence SNPs we required the following criteria: minor allele count >1, a minimum coverage of 4 and a minimum base quality of 20.

Using a custom Perl script and the full data set, we identified 2000 SNPs (minor allele count = 4; minimum coverage = 8; minimum base quality = 20) on chromsome 3R, which are separated by at least 10,500 bp.

We used a minimum base quality allowed of 25.

We used the SNP detection function in CLC Genomics Workbench, based on the neighborhood quality standard (NQS) algorithm, using the following parameters: minimum coverage = 5; minimum central base quality = 30; average base quality over a window length of 11 nucleotides = 15; and, minimum allele frequency = 35%.

The minimum read base quality value (--QRL) aggregateum alleleate allele quality value (--QAL) flags had to be set to a zero threshold because the assembly software used assigns low base quality scores to the consensus sequence at positions where there is a high degree of variability, such as at SNPs [ 40].

Single-base substitutions were called using SAMtools and filtered by coverage (minimum 10, maximum 150), read quality (minimum quality, 30), mapping quality (minimum quality, 30), base quality (minimum quality, 30), and end of contig (minimum distance to end of contig, 500 bp).

Prinseq-lite 0.20.04 (Schmieder and Edwards 2011) was used for quality control and filtering of reads (minimum read length of 50 nt, minimum average base quality of 25, maximum ambiguous nt (N) of 1) after which the data were used for SSR mining.

Variants with minimum coverage of six reads with minimum base calling quality (Q) of 30 at the respective position, a minimum SNP-call quality (QUAL) of 160 (QUAL = −10 log10 (probability of wrong call) [ 56]) and with more than 67% of all quality reads calling the SNP were retained.