What are good alternatives to the GATK IndelRealigner tool?
Specially considering CPU and memory requirements in comparison to GATK.
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There is SRMA, which performs the same task. I don't know how it compares in terms of computational requirements.
I have tried both SRMA and GATK indel aligner and found GATK indel aligner easy to use and found it to be faster than SRMA.
Thanks, this is very useful information.
I downloaded the code, thanks. Is there a way to run it that mimics the parameters used in a gatk realigner run? java -Djava.io.tmpdir="/tmp" -Xmx4g -jar "GATK/GenomeAnalysisTK.jar" -et NO_ET -T RealignerTargetCreator -R "genome.fa" -I "file.bam" -o "file.intervals" -L region
Not that I know of. They actually use different sets of reads for realignment.
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