vcfr

[…] roach to infer copy number based on the frequency that the most abundant and second most abundant alleles were sequenced at. While we designed this method to work with VCF data () using the R package vcfR (), we feel an important role of our method is to help make this data available to the existing universe of R packages. VCF data only includes information on variable positions within the genome. […]

[…] well as a type of decline (one linear and two exponentials; see Table ). For each scenario, the minor allele frequencies were calculated for both Finges 1940 and 1950 populations using the R‐package vcfR (Knaus & Grünwald, ). Then, starting from the minor allele frequency distribution of Finges 1940, we simulated a new minor allele frequency distribution based on the described scenarios of popula […]

[…] eMEAN models to identify ions that were shared by both models (Venny version 2.1; ).Finally, we generated a heat map of molecular masses and intensities for each averaged spectrum using the R package vcfR by applying a mass tolerance of 1 Da and a minimum relative abundance of 5%. Molecule relative abundance was log2 transformed to aid visualization of rare molecules. As described above, the abund […]

[…] 7 HaplotypeCaller and the options ‘-ERC GVCF -ploidy 1’ were used to call variants for each isolate, and the data were then combined using GenotypeGVCFs (). Variants were filtered using the R package vcfR with depth filtering using quantile probabilities of 0.25 and 0.75 as cutoffs and a minimum of four reads, as well as a missing data cutoff of 20% (). Variants were converted into a fasta alignme […]