Sentence examples for minimum variant call from inspiring English sources
The higher specificity value achieved by Dindel is likely due to the minimum variant call threshold used in analysis.
Minimum coverage for a variant call was set at 5, and maximum was set at 150.
In each case, the minimum score for variant calls was automatically set to the value where the density of scores >0 attains its first first local minimum.
Single nucleotide variants and short insertions and deletions (indels) were called using SAMtools mpileup [Li et al., 2009] and bcftools and quality-filtered to require a minimum 20% of reads supporting the variant call.
After splitting the maps at these low-coverage regions, we used OMBlast to align the split fragments with a minimum of 10 signals to reference maps and to detect large insertions, deletions, and inversions using partial-alignment-based strategy as described below, except that the minimum number of fragments supporting the variant call was set to one.
The resulting variant call format (VCF) file is then filtered for minimum coverage and minimum allele proportion.
14 Briefly, genotypes of SNPs at HapMap Phase II loci 17, 18 were inferred using GATK UnifiedGenotyper 19, 20 with a required minimum depth of 10 reads per sample, to produce variant call format (VCF) files.
By using an alternative variant calling approach (a minimum read depth of 50 and a minimum variant frequency of 4%%) a recent study demonstrated the rapid expansion and collapse of different sub-populations that evolved in parallel during the evolution of extensively drug resistant (XDR-TB) [ 14].
BAM files generated from Bowtie2 mapping were used as inputs for the variant detection function in CLC Genomics Workbench to call mismatches with a minimum read depth of 100× and a minimum variant frequency of 20%%.
SNP calling parameters were set to minimum coverage = 5, and minimum variant frequency = 0.2.
More than 90% of the FP calls were eliminated by filtering with a coverage > 2 and a minimum variant frequency > 35% for the heterozygous SNPs identified by CLC.
