RealignerTargetCreator inputs multiple Bams??

Question: RealignerTargetCreator inputs multiple Bams??

3.7 years ago by

Pakistan

micro32uvas • 10 wrote:

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

realignertargetcreator bam gatk • 1.3k views

ADD COMMENT • link •

modified 3.7 years ago by Devon Ryan ♦ 98k • written 3.7 years ago by micro32uvas • 10

3.7 years ago by

agoel • 30

agoel • 30 wrote:

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

ADD COMMENT • link written 3.7 years ago by agoel • 30

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

ADD REPLY • link written 3.7 years ago by Devon Ryan ♦ 98k

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

ADD REPLY • link modified 3.7 years ago • written 3.7 years ago by micro32uvas • 10

3.7 years ago by

Devon Ryan ♦ 98k

Freiburg, Germany

Devon Ryan ♦ 98k wrote:

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.

ADD COMMENT • link modified 3.7 years ago • written 3.7 years ago by Devon Ryan ♦ 98k

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

ADD REPLY • link written 3.7 years ago by micro32uvas • 10

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

ADD REPLY • link written 3.7 years ago by Devon Ryan ♦ 98k

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.

ADD REPLY • link modified 3.7 years ago • written 3.7 years ago by micro32uvas • 10

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.

ADD REPLY • link written 3.7 years ago by Devon Ryan ♦ 98k

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

ADD REPLY • link written 3.7 years ago by micro32uvas • 10

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.

ADD REPLY • link written 3.7 years ago by Devon Ryan ♦ 98k

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