Sentence examples for minimum coverage depth from inspiring English sources

We set a minimum coverage depth requirement to reduce the impact of sampling variance on genotype calling and focus primarily on how platform specific differences in allele ratio balance and/or quality.

Valid comparisons were defined as those where a) Illumina genotype data was present for the individual at the base position and b) the sequencing data for the corresponding position had a minimum coverage depth of 20×.

JN637766) using the Alignreads pipeline version 2.25 (Straub et al., 2011) with the following options: percent identity = medium, minimum coverage depth = 5, and single nucleotide polymorphism (SNP) minimum coverage depth = 25 with 80% of those reads supporting the SNP.

During variant calling we required a minimum coverage depth of 20 and minimum number of variants reads of 5 to call SNVs or indels.

We calculated that a minimum coverage depth of 22 reads was required to produce an accurate consensus sequence for FMDV O.

The 20 BLAST-annotated contigs with the largest numbers of reads contained 301 SNPs with alternate alleles in at least 20% of reads and minimum coverage depth of 10×.

Under the criteria of minimum coverage (read depth) of four and the minimum variant frequency of two, the variations compared to the reference sequence were counted as SNPs.

Therefore, according to our experience, a minimum 30× coverage depth is required for reliable detection of variants for diagnostic purposes.

2) All reads at the SNP locus had a minimum read coverage depth ≥ 8 to exclude putative SNPs that were based on too few reads.

To build Venn Diagrams, the following filtering criteria were used: for somatic SNVs we required a minimum of 20X coverage depth with ≥5 variant reads from all tumor and normal samples, for indels we used coverage depth cutoff of 20 and variant reads of five for tumor samples.

SNP filtering was performed in two steps, first using SAMtools'varFilterer' command specifying fairly permissive minimum quality cutoffs, coverage depth min/max cutoffs of 4 and 100, as well as options to disqualify SNPs that are too close to each other (as required by Illumina's GoldenGate Assay).