getGATKInfo: Get GATK info tags
In bahlolab/moimix: Estimating mulitplicity of infection from high-throughput sequencing data
Description
Usage
Arguments
Value
References
View source: R/seqarray_process_helpers.R
Description
Obtain GATK info tags relevant to best practices.
Usage
1
getGATKInfo(gdsfile)
Arguments
gdsfile
a SeqVarGDSClass object
Value
a data.frame with the following columns:
chromosome
position
variant.id
qd - (average quality by depth)
mq - RMS mapping quality
fs - Fisher strand bias
mqrank - MQ rank
haplotypescore
readposranksum
References
http://gatkforums.broadinstitute.org/gatk/discussion/2806/howto-apply-hard-filters-to-a-call-set
bahlolab/moimix documentation built on April 16, 2020, 8:40 a.m.
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Description Usage Arguments Value References
View source: R/seqarray_process_helpers.R
Description
Obtain GATK info tags relevant to best practices.
Usage
1 | getGATKInfo(gdsfile)
|
Arguments
gdsfile |
a |
Value
a data.frame with the following columns: chromosome position variant.id qd - (average quality by depth) mq - RMS mapping quality fs - Fisher strand bias mqrank - MQ rank haplotypescore readposranksum
References
http://gatkforums.broadinstitute.org/gatk/discussion/2806/howto-apply-hard-filters-to-a-call-set
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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