realignIndelsGATK: Realign indels via GATK
In HTSeqGenie: A NGS analysis pipeline.
Description
Usage
Arguments
Details
Value
Author(s)
Description
Realing indels using the GATK tools RealignerTargetCreator
and IndelRealigner.
Requires a GATK compatible genome with a name matching
the alignment genome to be installed in 'path.gatk_genome'
Usage
1
realignIndelsGATK(bam.file)
Arguments
bam.file
Path to bam.file
Details
Since GATKs IndelRealigner is not parallelized, we run it in
parallel per chromosome.
Value
Path to realigned bam file
Author(s)
Jens Reeder
HTSeqGenie documentation built on Nov. 8, 2020, 6:12 p.m.
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Description Usage Arguments Details Value Author(s)
Description
Realing indels using the GATK tools RealignerTargetCreator and IndelRealigner. Requires a GATK compatible genome with a name matching the alignment genome to be installed in 'path.gatk_genome'
Usage
1 | realignIndelsGATK(bam.file)
|
Arguments
bam.file |
Path to bam.file |
Details
Since GATKs IndelRealigner is not parallelized, we run it in parallel per chromosome.
Value
Path to realigned bam file
Author(s)
Jens Reeder
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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