new_STRAND: new_STRAND
In pllittle/UNMASC: Tumor-Only Variant Calling with Unmatched Normal Control Samples
new_STRAND R Documentation
new_STRAND
Description
Extracts strand-specific read counts from a
bam file.
Usage
new_STRAND(BAM_fn, vcs, minBQ = 13, minMQ = 40, NT = 1)
Arguments
BAM_fn
A character string for the bam's file path.
vcs
A R data.frame of variant calls containing
columns Chr, Position, Ref, and
Alt corresponding to the chromosome,
genomic position, reference base(s), and alternate base(s),
respectively.
minBQ
An integer for minimum base quality.
minMQ
An integer for minimum mapping quality.
NT
A positive integer for the number of threads.
pllittle/UNMASC documentation built on June 1, 2025, 1 p.m.
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| new_STRAND | R Documentation |
new_STRAND
Description
Extracts strand-specific read counts from a bam file.
Usage
new_STRAND(BAM_fn, vcs, minBQ = 13, minMQ = 40, NT = 1)
Arguments
BAM_fn |
A character string for the bam's file path. |
vcs |
A R data.frame of variant calls containing
columns |
minBQ |
An integer for minimum base quality. |
minMQ |
An integer for minimum mapping quality. |
NT |
A positive integer for the number of threads. |
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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