h5vc (version 2.6.3)

Managing alignment tallies using a hdf5 backend

Description

This package contains functions to interact with tally data from NGS experiments that is stored in HDF5 files. For detail see the webpage at http://www.ebi.ac.uk/~pyl/h5vc.

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Version

2.6.3

License

GPL (>= 3)

Maintainer

Paul Theodor Pyl

Last Published

February 15th, 2017

Functions in h5vc (2.6.3)

binGenome

Function for binning a genome.

Estimate allelic frequency distributions in bins along the genome

mismatchPlot

callVariantsSingle

Single sample variant calling

mergeTallyFiles

Merging multiple tally files into one

h5dapply

writeReference

Filling the Reference dataset in a tally file from a DNAString

applyTallies

Preparing the results of tallyBAM for writing to an HDF5 tally file

prepareTallyFile

writeToTallyFile

Writing data to an HDF5 tally file

h5vc-package

Managing alignment tallies using a hdf5 backend

tallyRanges

Tallying function with a GRanges interface.

batchTallies

Tallying bam files in parallel using BatchJobs on high performance compute clusters (HPC)

Paired variant calling using fisher tests

prepareForHDF5

Preparing the results of tallyBAM for writing to an HDF5 tally file

plotMutationSpectrum

Plotting a mutation spectrum

callVariants

Variant calling

mutationSpectra

Mutation spectrum analyses

mergeTallies

Merging the prepared results from multiple bam file tallies into one block that can be written to the HDF5 tally file

getSampleData

Reading and writing sample data from / to a tally file