RealignerTargetCreator inputs multiple Bams??

Question

[micro32uvas]

Hello Everyone,

I have been working with RealignerTargetCreator and in its pages, RealignerTargetCreator. It states that it takes multiple inputs as Bam. But its not taking it. when I checked Galaxy.it stated that GenomeAnalysisTK: RealignerTargetCreator accepts an aligned BAM input file.

I want to give all my Bam files for indel realigner intervals.

Here's the command that I am using; java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R reference.fasta -I input.bam -known indels.vcf -o forIndelRealigner.intervals

Your help is appreciated. Qurat

Answer 1

[agoel]

For using multiple bam files as inputs to RrealignerTargetCreator, you can use "-I input1.bam -I input2.bam -I input3.bam" in the command.

[Devon Ryan]

This is in Galaxy, micro32uvas can't issue commands.

[micro32uvas]

You just solved my problem Pearl :) I'll get back here, if there's still some errors

Answer 2

[Devon Ryan]

There's a separate biostar site for Galaxy. Anyway, I would strongly encourage you NOT to use GATK in Galaxy, it doesn't follow GATK's best practices. Use freeBayes or samtools instead.

BTW, what you're trying to do isn't possible in the Galaxy wrapper.

[micro32uvas]

I never prefer Galaxy anyways, and yes its very limited as well. Its just I was missing the -I switch everytime, which was creating the problem. I just checked in galaxy for the given options there, if i was missing any.

Thanks Devon

[Devon Ryan]

Ah, if you're already using the command line then use the HaplotypeCaller and then skip this step entirely.

[micro32uvas]

Can you kindly elaborate this Devon? Actually i am working on Haplotypecaller but along with this preprocessing phase. i.e. after marking duplicates, now i am up with realign target creator, indel realigner and then base calibration. Then would be the haplotype calling using haplotype caller.

Your help at this stage would be epic for my work

P.S. I am already on command line.

[Devon Ryan]

If you're using the HaplotypeCaller then you don't need to align around indels. There's also no need to perform base quality recalibration any more. This will save you from wasting a LOT of time for no benefit.

[micro32uvas]

i cannot understand how would this omit realignment. wouldn't realigner give further improvement in terms of mapping and enhanced calibration. If you could precisely share the command that would cover all of it, it would be highly appreciated

[Devon Ryan]

Why realignment isn't needed requires explaining how the HaplotypeCaller and indel realignment work. I'll just link to this article on the GATK site, which goes over the process in more detail than would fit in a comment. Suffice it to say, indel realignment is already part of the HaplotypeCaller.

Regarding base recalibration, the head to head comparisons that Brad Chapman has shown (have a look at his blog, he documents everything there) that this isn't really beneficial any more. I know it's still in the GATK "best practices", but those seem to only be slowly updated.