QD: Plot Quality by Depth (QD)
In Hatoonli/vcfqc: What the Package Does (One Line, Title Case)
QD R Documentation
Plot Quality by Depth (QD)
Description
This is the variant confidence (from the QUAL field) divided by the unfiltered depth of non-hom-ref samples. This annotation is intended to normalize the variant quality in order to avoid inflation caused when there is deep coverage. For filtering purposes it is better to use QD than either QUAL or DP directly. The generic filtering recommendation for QD is to filter out variants with QD below 2.
Usage
QD(f, n)
Arguments
f
VCF input file
n
Threshold value (optional), default is the recommended GATK value.
Value
A plot of QD score and frequency
with table summary
and number of variants falling outside the threshold
Hatoonli/vcfqc documentation built on May 16, 2022, 12:19 p.m.
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| QD | R Documentation |
Plot Quality by Depth (QD)
Description
This is the variant confidence (from the QUAL field) divided by the unfiltered depth of non-hom-ref samples. This annotation is intended to normalize the variant quality in order to avoid inflation caused when there is deep coverage. For filtering purposes it is better to use QD than either QUAL or DP directly. The generic filtering recommendation for QD is to filter out variants with QD below 2.
Usage
QD(f, n)
Arguments
f |
VCF input file |
n |
Threshold value (optional), default is the recommended GATK value. |
Value
A plot of QD score and frequency with table summary and number of variants falling outside the threshold
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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