View source: R/RegressHaplo_workflow.R
bam_to_variant_calls.pipeline | R Documentation |
Given a bam file, create variant call file
bam_to_variant_calls.pipeline( bam_file, out_dir, start_pos = NULL, end_pos = NULL, sig = 0.01, heavy_tail = T )
bam_file |
path to bam file |
out_dir |
output directory, will be created if needed. variant call file will be placed in the output directory |
start_pos |
position on reference at which to start looking for variant calls |
end_pos |
position on reference at which to end looking for variant calls |
sig |
significance level at which variants will be called. An automatic bonferroni correction is applied to account for the number of positions in the reference. |
heavy_tail |
If T, then a betabinomial is used to call errors following Gerstung et al 2011. If F, then a poisson is used to call variants following Wang et al 2007 |
variant calls are given by a data.frame with 6 columns named c("pos", "A", "C", "G", "T", "-") pos gives the position at which a true variant exists. The other columns have logical entries, with TRUE meaning that a true variant exists with the corresponding nucleotide.
path to variant call file
Wang,C. et al. (2007) Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance. Genome Res., 17, 1195–1201,
Gerstung et al. (2011) Reliable detection of subclonal single-nucleotide variants in tumour cell populations. Nature Communications.
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