get_lsingle_vcf: Function to parse Phred-scaled likelihoods
In Struglab/RVS: Robust Variance Score (RVS) test for association of variants from next generation sequence data with binary traits using external controls
Description
Usage
Arguments
Value
Description
This function parses the data column (GT:AD:DP:GQ:PL) to get the PL values -10log10(x),
and converts them to a vector of likelihoods: L0,L1,L2. It's called within get_likelihood_vcf.
newer version of workflow of GATK suggested calling the BAM for each individual first then combined them,
so the format column can have different length for each variant like the example Lizhen provided.
Usage
1
get_lsingle_vcf(Mij, n_pl)
Arguments
Mij
a single data unit of format'GT:AD:DP:GQ:PL'.
n_pl
an integer to indicate the PL field.
Value
a vector of three values: l0, l1, l2
Struglab/RVS documentation built on May 9, 2019, 3:11 p.m.
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Description Usage Arguments Value
Description
This function parses the data column (GT:AD:DP:GQ:PL) to get the PL values -10log10(x),
and converts them to a vector of likelihoods: L0,L1,L2. It's called within get_likelihood_vcf.
newer version of workflow of GATK suggested calling the BAM for each individual first then combined them,
so the format column can have different length for each variant like the example Lizhen provided.
Usage
1 | get_lsingle_vcf(Mij, n_pl)
|
Arguments
Mij |
a single data unit of format'GT:AD:DP:GQ:PL'. |
n_pl |
an integer to indicate the PL field. |
Value
a vector of three values: l0, l1, l2
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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