Alternatives To Gatk Indelrealigner?

Question

[14134125465346445]

What are good alternatives to the GATK IndelRealigner tool?

http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_indels_IndelRealigner.html

Specially considering CPU and memory requirements in comparison to GATK.

Answer 1

[Anders Bergström]

There is SRMA, which performs the same task. I don't know how it compares in terms of computational requirements.

[Ashutosh Pandey]

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.

[14134125465346445]

Thanks, this is very useful information.

Answer 2

[Sean Davis]

https://github.com/ekg/ogap

[14134125465346445]

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

[Sean Davis]

Not that I know of. They actually use different sets of reads for realignment.