variant_calls_cutoff: Returns variant calls given a VSeqTools_pileup object
In SLeviyang/RegressHaplo: Haplotype Reconstruction Using Penalized Regression
variant_calls_cutoff R Documentation
Returns variant calls given a VSeqTools_pileup object
Description
Given a pileup, variants with variability above min_freq are
identified. This is a simple variant caller which is much faster
than VPhaser2, but cannot call low frequency variants with precision
since phasing information is not used
Usage
variant_calls_cutoff(pu, min_freq = 0.03)
Arguments
pu
a VSeqTools_pileup object returned by BAM_pileup
min_freq
Minimum frequency above which a variant is called.
Value
A VSeqTools_variant_call object which inherits the data.frame class.
VSeqTools_variant_call objects are
data.frames with
columns pos, A, C, G, T, d, i. pos gives the position on
the reference. Entries in other columns are logical depending
on whether associated variant/deletion/insertion is called
Warning: Currently uses the df data.frame in VSeqTools_pileup
object. Needs to be extended to allow for different strands.
SLeviyang/RegressHaplo documentation built on June 1, 2022, 10:48 p.m.
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| variant_calls_cutoff | R Documentation |
Returns variant calls given a VSeqTools_pileup object
Description
Given a pileup, variants with variability above min_freq are identified. This is a simple variant caller which is much faster than VPhaser2, but cannot call low frequency variants with precision since phasing information is not used
Usage
variant_calls_cutoff(pu, min_freq = 0.03)
Arguments
pu |
a VSeqTools_pileup object returned by BAM_pileup |
min_freq |
Minimum frequency above which a variant is called. |
Value
A VSeqTools_variant_call object which inherits the data.frame class. VSeqTools_variant_call objects are data.frames with columns pos, A, C, G, T, d, i. pos gives the position on the reference. Entries in other columns are logical depending on whether associated variant/deletion/insertion is called
Warning: Currently uses the df data.frame in VSeqTools_pileup object. Needs to be extended to allow for different strands.
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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