MQ: Plot Mapping Quality (MQ)
In Hatoonli/vcfqc: What the Package Does (One Line, Title Case)
MQ R Documentation
Plot Mapping Quality (MQ)
Description
This is the root mean square mapping quality over all the reads at the site. Instead of the average mapping quality of the site, this annotation gives the square root of the average of the squares of the mapping qualities at the site. It is meant to include the standard deviation of the mapping qualities. Including the standard deviation allows us to include the variation in the dataset. A low standard deviation means the values are all close to the mean, whereas a high standard deviation means the values are all far from the mean.When the mapping qualities are good at a site, the MQ will be around 60.
Usage
MQ(f, n)
Arguments
f
VCF input file
n
Threshold value (optional), default is the recommended GATK value.
Value
A plot of MQ 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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| MQ | R Documentation |
Plot Mapping Quality (MQ)
Description
This is the root mean square mapping quality over all the reads at the site. Instead of the average mapping quality of the site, this annotation gives the square root of the average of the squares of the mapping qualities at the site. It is meant to include the standard deviation of the mapping qualities. Including the standard deviation allows us to include the variation in the dataset. A low standard deviation means the values are all close to the mean, whereas a high standard deviation means the values are all far from the mean.When the mapping qualities are good at a site, the MQ will be around 60.
Usage
MQ(f, n)
Arguments
f |
VCF input file |
n |
Threshold value (optional), default is the recommended GATK value. |
Value
A plot of MQ 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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